There has been greater societal awareness of differences in gender identity and sexual orientation in recent years. The rates of identifying as transgender or gender non-conforming (TGNC) are increasing and are known to be higher in the younger population and will therefore be over-represented in the inflammatory bowel disease (IBD) subpopulation. However, despite this there is very little in the literature with regards to those who identify as TGNC and are diagnosed with IBD (TGNC-IBD). Many TGNC individuals have poor experiences when seeking healthcare and many physicians find it a challenging and daunting clinical situation to be faced with. We reviewed the available literature with regards to TGNC-IBD population demographics, physical, mental and sexual health considerations, medication interactions and implications for surgery in this heterogenous group. We have identified areas that need further research and suggested simple and practical steps that can be adopted in order to help healthcare providers improve the experience for TGNC individuals diagnosed with IBD and the quality of care they provide.