The present study aims to study gender dysphoria, sexual health communication, and healthcare challenges within the transgender community, owing to the dearth of studies on this topic, especially in the North Indian context. The objective is to examine the intersectional dynamics of psychological well-being, social support, and healthcare utilization in the context of the three variables. Using a mixed method design, 115 participants were recruited from Delhi and Uttar Pradesh. The tools used were the Gender Dysphoria Scale, a general health questionnaire, the Health Protective Sexual Communication Scale, in-depth interviews, and focus group discussion. The analysis showed a high level of gender dysphoria, above-average overall health, and below-average communication level concerning sexual health and sexually transmitted diseases (STDs). A significant positive correlation was found between the general health questionnaire and the Health Protective Sexual Communication Scale, suggesting that better communication led to better health practices. The level of education seemed to impact protective health communication. The qualitative analysis further uncovered manifestations of gender dysphoria in overall health. Social, emotional, financial, and systemic support played a pivotal role in the participants’ well-being and healthcare-seeking behaviors. Therefore, advocacy for inclusive healthcare policies, government funding or support, enhancement of infrastructure, and inclusive environment in schools is suggested in order to dismantle taboos hindering sexual health discussions.