Background A significant high proportion of men engage in sexual relationships with other men has been observed in the country, which has direct linkage with the physical and the mental health status of this population. The population is more at risk when it is associated with migrant MSMs, having the characteristics of bridge population, due to associated migrant as well as MSM health related issues. Due to their unique health care needs, the population repeatedly remains devoid of basic health care services. The purpose of the study is to highlight their overlooked health issues, barriers to care and stigma associated with migrant MSMs. Methods A cross-sectional qualitative in-depth interviews were conducted with 62 migrated MSMs in New Delhi in the Month of November-December 2012. The snow-bowling method is used to track the hidden population. Interviews were based on pre decided themes of health Issues, service availability, barriers to care and stigma associated. Data was analysed by using thematic framework approach. New emerging issues verbatim were highlighted and the case narrative has been done. Results The majority of the participants of the study reported that they were not aware about the health care service availability even if they are willing to get screened. Most of the participants perceived that they are suffering with the mental disorders but because of stigma associated, along with the other healthcare need, they couldn't able to avail the mental health services. Occupational hazard was also reported in the majority of the cases. Conclusion Special attention to mental health care is required along with a comprehensive package also dealing with the physical as well as the social well being of MSMs. Special attention is required for their screening since the population being migrant is much more at risk when compared to migrant and MSM individually.