More than 13,500 transgender and non-binary adults are on waiting lists for NHS gender identity clinics in England.
Some people have had to wait three years for their first appointment at a clinic, BBC research has found.
The system has been described as "broken" by an ex-soldier who has been waiting to see a consultant since 2016.
There has been a 40% increase in referrals over the past four years and NHS England said it had increased investment amid rising demand.
NHS England has pledged to bring waiting times to below 18 weeks but the average wait for a first appointment at a gender identity clinic is 18 months, according to national charity LGBT Foundation.
Andrea Halliley, 51, went on tours to Northern Ireland, Bosnia and Iraq before retiring from the army in 2014.
She went to her GP in September 2016 and was referred to the NHS gender identity service in Leeds, having a telephone assessment in July 2017 and an appointment with a psychiatric nurse in December the following year.
Ms Halliley, from County Durham, is currently waiting for an assessment with a consultant and has been told it could be February or March 2020 at the earliest.
She said: "Life is pretty much hell - you are living everyday a battle within yourself no matter what's going on outside.
"Inside yourself there's a war raging between who you are presenting yourself and who you really are.
"The longer and longer it's dragged out you're made to feel marginalised and you're made to feel that you're not important."
Gender identity clinics offer assessment and support to people aged 18 and above with gender dysphoria, a condition in which a person experiences discomfort or distress because there is a mismatch between their biological sex and gender identity.
They offer services on the NHS including hormone treatment, facial hair removal, genital hair removal prior to surgery, voice coaching, speech and language therapy and psychological support.
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There are seven NHS gender identity clinics for adults in England, located in Sheffield, London, Nottingham, Northumberland, Devon, Northamptonshire and Leeds.
All of the clinics provided the BBC with data on referrals over several years except Leeds, with the BBC using figures detailed in board minutes.
Emma Meehan, assistant director of public affairs at the LGBT Foundation, said: "We are disappointed, but unfortunately not surprised, to hear of these findings.
"Currently the NHS is falling drastically short when it comes to supporting trans and non-binary people.
"NHS Guidelines say 18 weeks is the limit from referral to treatment. In reality the average waiting time for a first appointment with a gender identity clinic is 18 months."
An NHS England spokesperson said: "Demand for gender identity services continues to rise as more people feel able to come forward for support and treatment, and we've increased investment to respond to the rising demand, with staff working hard to reduce waiting times for patients and support people who are on waiting list."
If you or someone you know has been affected by a gender identity issue, help and support is available at bbc.co.uk/actionline