Medicated vs natural frozen embryo transfer (& FET timeline from start to finish)

For many fertility patients, a frozen embryo transfer (FET) experience is very different from IVF stimulation and egg collection. The injections may be fewer, the appointments less intense, and yet emotionally, the stakes often feel even higher. TRB founder and CEO Eloise has had five embryo transfers across almost a decade, and each time, a totally different story unfolded. 

By the time you reach transfer day, you may already have navigated months – or years – of fertility treatment. You have embryos waiting, hopes building – and a lot of questions about what exactly is happening inside your body.

Digging deeper

IVF is full of decisions, not least whether to go for a medicated FET, or natural. 

What does a medicated frozen embryo transfer look like, on paper, versus a natural transfer? What medications are involved? And what actually happens between embryo transfer and that long-awaited pregnancy test?

To help demystify the process, we spoke to Miss Shirin Khanjani, Co-Founder and Medical Director of Fitzrovia Fertility, about the different frozen embryo transfer protocols available, how clinics decide which approach is best, and what patients can expect every step of the way.

Keen to connect with Fitzrovia Fertility? Located in the heart of London, the clinic combines cutting-edge reproductive science with a trademark compassionate approach – from fertility assessment, IVF, PGT-A and fertility preservation to expertise in recurrent pregnancy loss, endometrial PRP and genetic counselling, the team are across it.

First things first: What is FET?

FET stands for frozen embryo transfer.

Rather than transferring an embryo during the same cycle as egg collection, embryos are frozen and transferred later in a separate cycle.

This approach has become increasingly common in UK fertility treatment. Advances in embryo freezing technology have revolutionised survival rates, allowing clinics and patients to focus on creating the best possible environment inside the uterus before transfer takes place.

For many patients, FET follows a previous IVF cycle, although frozen embryos may also have been created through donor conception, fertility preservation or previous treatment attempts.

How many days after egg retrieval is embryo transfer?

If you are having a fresh embryo transfer, transfer typically occurs between three and five days after egg retrieval.

However, in a frozen embryo transfer cycle, the timeline is very different.

Embryos are frozen after fertilisation and development in the laboratory, then transferred weeks, months or even years later. Some patients have a transfer the following month, while others return to their embryos after completing medical treatment, or navigating other milestones and life events. 

Having recently supported my husband through four cycles of chemotherapy and major surgery, I’ve looked into the realities here a great deal.

Medicated vs natural frozen embryo transfer

One of the biggest decisions during treatment planning is whether to proceed with a natural FET or a medicated FET.

Both approaches aim for the same outcome: a receptive uterine lining that is perfectly synchronised with the embryo being transferred.

The difference lies in how that lining is prepared.

Natural FET

In a natural cycle, your clinic works with your body’s own hormones.

Ovulation occurs naturally, and transfer timing is carefully matched to your body’s natural implantation window. Monitoring often involves multiple scans and blood tests to identify exactly when ovulation takes place.

Medicated FET

In a medicated cycle, ovulation is suppressed or bypassed. Hormones are provided through medication to build the lining and create optimal conditions for implantation.

This approach offers greater predictability and scheduling flexibility and is often recommended for patients with irregular cycles or ovulation difficulties.

So, the key question for patients – how do you choose the right FET protocol? Keep reading for our expert Q&A with Fitzrovia Fertility MD and co-founder, Dr Shirin Khanjani.  

How do you decide on the protocol, and how does the timeline start?

Dr Khanjani says: There’s no single “right” frozen embryo transfer (FET) protocol – the right approach depends on the individual patient.

At Fitzrovia Fertility, we look at the whole picture: menstrual regularity, previous treatment history, age, lifestyle factors, previous implantation outcomes and, importantly, whether a patient ovulates naturally.

I increasingly favour a natural or modified natural FET where appropriate. Emerging evidence suggests that maintaining the body’s own ovulation and corpus luteum may have important benefits for placentation and pregnancy health. 

However, a medicated FET remains an excellent option for many patients, particularly those with irregular cycles, anovulation, PMOS/PCOS, premature ovarian insufficiency, or people who need more flexibility in their scheduling.

The decision is always individualised rather than going for one-size-fits-all protocols.

What’s the difference between a medicated and natural FET?

Dr Khanjani says: In a natural FET, we work with your body’s own cycle. Ovulation occurs, a corpus luteum forms, and the timing of embryo transfer is aligned with your natural hormonal changes.

In a medicated FET, ovulation is bypassed and synthetic hormones are used to prepare the uterine lining and support implantation.

Historically, medicated cycles became popular because they are highly predictable and easier to schedule. However, recent research has highlighted that the absence of a corpus luteum may contribute to higher rates of hypertensive disorders of pregnancy, including pre-eclampsia, compared with ovulatory FET cycles.

For this reason, whenever it is clinically appropriate, we actively explore whether a natural or modified natural cycle may be suitable.

Frozen embryo transfer medication timeline

Dr Khanjani says: Although every clinic protocol varies slightly, a medicated frozen embryo transfer timeline generally follows a similar structure:

Days 1-3: Period begins

Your menstrual cycle starts (naturally or via medication) and your clinic confirms treatment plans.

Depending on your protocol, FET medications may begin during the first few days of bleeding.

Days 2-14: Oestrogen phase

The first stage focuses on building the uterine lining.

How does oestrogen support the uterine lining, and what medications are used?

In a medicated cycle, oestrogen is used to prepare the endometrium, creating the environment required for implantation.

The most commonly used medications include oral or vaginal oestradiol tablets or transdermal patches. At Fitzrovia Fertility, we tailor the route according to patient preference, previous response and side-effect profile.

The aim is to develop an appropriately thick, healthy, receptive endometrium with the appropriate appearance on ultrasound.

Around day 10-14: Lining scan

Once enough oestrogen has been taken, clinics assess whether the lining is ready for the next stage.

How and when is the uterine lining monitored?

For a medicated FET, we typically perform ultrasound monitoring after around 10 days of oestrogen treatment. At this appointment, we assess both the thickness and appearance of the endometrium. 

Whilst there is no absolute cut-off, we’re looking for a lining that appears appropriately developed and receptive, before introducing progesterone. We’re also checking that the ovaries remain “quiet” and that there hasn’t been any unexpected follicular development that might alter the treatment plan.

For a natural or modified natural FET, the process is slightly different. Because we’re working with the body’s own cycle, monitoring is generally more intensive and often involves several scans over a number of days. We track the growth of the leading follicle, monitor changes within the endometrium, and frequently use blood tests to assess hormone levels, particularly LH and progesterone. 

The aim is to accurately identify ovulation, or time a trigger injection if using a modified natural approach, so that embryo transfer can be synchronised precisely with the body’s natural implantation window.

If the lining isn’t responding as expected, what adjustments can be made?

One of the advantages of a personalised approach is that there are numerous options before abandoning a cycle. We may increase the oestrogen dose, change the route of administration, extend the duration of treatment, or combine different forms of oestrogen.

For patients with persistently thin endometrium, we may consider additional strategies such as vaginal oestrogen, vitamin E, pentoxifylline, optimisation of thyroid function and metabolic health, acupuncture support, or selected adjunctive treatments like PRP where appropriate. 

Rather than applying a rigid protocol, we aim to understand why the lining isn’t responding and tailor treatment accordingly.

Then, progesterone begins

Once the lining is ready, progesterone is introduced.

Why is progesterone timing so important?

Progesterone timing is arguably one of the most important aspects of a frozen embryo transfer cycle.

Once progesterone is started, the endometrium begins a carefully orchestrated sequence of changes that creates the implantation window. The embryo must arrive at precisely the right stage.

For example, a day-5 blastocyst typically requires five full days of progesterone exposure before transfer. Even small deviations in timing can potentially affect synchronisation between embryo and endometrium, which is why we place enormous emphasis on getting this right.

The days before transfer

While patients are often focused on transfer day itself, important changes are happening inside the uterus during the days beforehand.

What happens in the few days between starting progesterone and embryo transfer?

This is often the quietest stage from the patient’s perspective, but biologically a great deal is happening.

The endometrium transitions from a proliferative lining under the influence of oestrogen into a secretory lining under the influence of progesterone. Blood flow increases, implantation molecules are expressed and the uterus becomes receptive to embryo implantation.

Patients usually continue both oestrogen and progesterone throughout this period.

Embryo transfer

By contrast, embryo transfer day is often much simpler than patients realise – it usually revolves around a straightforward procedure that takes only a few minutes.

What should patients expect, on the day?

The embryo is loaded into a very fine catheter and transferred into the uterine cavity under ultrasound guidance, through the cervix. The procedure feels similar to a routine smear test – most patients find it significantly easier than expected, and don’t require sedation.

Following transfer, patients continue their hormonal support medications. Contrary to popular belief, bed rest is not required and normal gentle daily activities can be resumed immediately. Indeed, there is evidence to support that women who remain moderately active have higher chances of pregnancy. 

Immediately after transfer

Many patients become hyper-aware of every sensation in their body after transfer.

What is happening in the body?

Most patients feel completely normal. Some experience mild cramping (read our collab guide to cramping after IVF transfer for lots of specific support), bloating or pelvic awareness. Others notice breast tenderness, fatigue or nausea, although these symptoms are more commonly related to progesterone rather than implantation itself.

Importantly, the presence or absence of symptoms is not a reliable predictor of outcome.

How long does an embryo take to implant?

This is one of the most commonly searched questions during the two-week wait.

For a blastocyst transfer, implantation generally begins within one to three days after transfer and continues over several days as the embryo embeds within the uterine lining. By around seven to ten days after transfer, implantation is usually complete and hCG production has begun.

The emotional reality of the two-week wait

The period between transfer and pregnancy testing can feel endless.

Unlike stimulation cycles, with an FET there are often no appointments, scans or interventions. For many patients, this sudden lack of activity can feel surprisingly difficult.

What’s involved?

The two-week wait is often the most emotionally challenging part of treatment.

I believe strongly in supporting patients through this stage rather than simply telling them to wait. At Fitzrovia Fertility, we take a genuinely holistic approach. Alongside medical support, patients have access to our fertility coach, counsellor, nutritionist and acupuncture team.

I often encourage patients to anchor themselves in what they do know rather than what they cannot control. The embryo transfer is complete, and from this point much of the process is biological. Gentle exercise, maintaining routine, prioritising sleep and avoiding excessive symptom checking can all help make the wait more manageable.

Where does a long protocol IVF timeline fit in?

Dr Khanjani says: You may occasionally hear your clinician refer to a “long protocol” frozen embryo transfer cycle.

A long protocol usually refers to a medicated FET cycle, where the ovaries are first suppressed using medication before oestrogen is introduced.

Historically, this approach was used more commonly for women with endometriosis, adenomyosis, severe pelvic pain or recurrent implantation concerns.

While it remains useful in selected circumstances, it is not routinely required for all patients. As with every aspect of fertility treatment, the key is selecting the right protocol for the right patient.

Wrapping it up

Frozen embryo transfer has evolved significantly in recent years. While medicated cycles remain an important and highly effective option, increasing research is helping clinics better understand when natural or modified natural approaches may offer advantages.

As Dr Khanjani emphasises, the most important takeaway for patients is that there is no universally “best” protocol. The right medicated frozen embryo transfer timeline depends on your cycle, medical history, fertility diagnosis and personal circumstances.

Whether your treatment involves a natural cycle, a medicated cycle or a long protocol approach, success relies on one key principle: ensuring that embryo and endometrium are perfectly synchronised at the moment they meet. 

Understanding the timeline can make the process feel less overwhelming, and help you approach transfer day with greater confidence and clarity.

On your reading list

While you navigate (and wait!) put these reads on your stack: 

• What is ovarian reserve? Plus, everything to know about testing in London
• Yoga before embryo transfer – A senior instructor’s dos and don’ts 
• Cramping after IVF transfer? Don’t panic, here’s what to do
• Natural ovulation vs programmed regimens before FET: a multicentre, randomised clinical trial

Connect with Dr Khanjani and the team at Fitzrovia Fertility, to get the ball rolling on your next treatment cycle, whether it’s for the very first time, or a pivot.