Background. Maintaining optimal adherence to antiretroviral treatment (ART) is a challenge for adolescents with perinatally HIV (ALPHIV), and there is little consensus on what factors contribute to adherence in this population. This study assessed self-reported medication adherence among ALPHIV and explored structural factors that hinder or motivate them to adhere. Methods. This qualitative study used in-depth interviews with ALPHIV at the infectious disease control centre of a teaching hospital in Botswana. Thirty adolescents aged 12-19 years who were aware of their HIV status were recruited purposively. Transcribed interviews were analysed using the thematic approach and NVivo data analysis software. Findings. Nonadherence was a problem across age groups and gender. Perceived stigma was a major barrier to ART adherence. The fear of stigma and unintended disclosure were more pronounced in those attending boarding school. The adolescents were not willing to take medication in front of roommates and outside of the home. They opted for hiding and taking medication in privacy which led to missed doses. The heightened fear of being seen collecting ART medication affected keeping appointments for clinic visits. Fear of stigma also influenced the choice of action when there was a clash between school activities, dosing times, and scheduled clinic appointments for ART refill. The home environment was the main facilitator for adherence. Support was the strongest motivator for adolescents to adhere and keep up with clinic visits. On a personal level, the desire to be healthy and live long was a major motivator to adhere. Conclusions. The fear of stigma shaped the adolescents' adherence behaviour. Perceived stigma affected the time and place to take medication, the visit to the clinic for ART refill, and self-disclosure of HIV status. There is need to encourage adolescents to self-disclose their HIV status to friends since the fear of unintended disclosure fuelled perceived stigma. Planning of clinic appointments should also be consistent with realistic daily activities of adolescents.