Introduction. Sub-Saharan Africa is home to 89% of all young people living with HIV, a key population with specific challenges and needs. In-depth knowledge of service demands is needed to tailor and differentiate service delivery for this group. We evaluated HIV care preferences among young people living with HIV who were part of the PEBRA (Peer Educator Based Refill of ART) cluster-randomized trial. Methods. The PEBRA trial evaluated a novel model of care at 20 health facilities in Lesotho, Southern Africa. In the PEBRA model, a peer educator regularly assessed participant preferences regarding antiretroviral therapy (ART) refill location, SMS notifications (for adherence, drug refill, viral load), and general care support options and delivered services accordingly over a 12-month period. We present these preferences and their changes over time. Results. At enrolment, 41 of 123 (33.3%) chose ART refill outside the health facility, compared to 8 of 123 (6.5%) after 12 months. Among those selecting clinic-based ART refill, many preferred collecting ART during the peer educator led Saturday clinic club, 45 of 123 (36.5%) at the beginning and 55 of 123 (44.7%) at the end. SMS reminders for treatment adherence and ART refill visits were chosen by 51 of 123 (41.5%) at enrolment and 54 of 123 (44.7%) at the last assessment. Support by the peer educator was popular at the beginning (110 of 123 (89.4%)) and lower but still high at the end (85 of 123 (69.1%)). Thirteen of 123 (10.6%) participants chose support by the nurse, without the involvement of any peer educator, at the first and 21 of 123 (17.1%) at the last assessment. Conclusion. Our longitudinal preference assessment among young people living with HIV in Lesotho showed a sustained interest in SMS notifications for adherence and refill visits as well as in additional support by a peer educator. ART refill outside the health facility was not as popular as expected; instead, medication pick-up at the facility, especially during Saturday clinic clubs, was favoured. The PEBRA trial was registered with clinicaltrials.gov (NCT03969030. Registered on 31 May 2019)