BACKGROUND: A large proportion of abortion-related mortality and morbidity occurs in the second trimester of pregnancy. The Uganda Ministry of Health policy restricts management of second-trimester incomplete abortion to physicians who are few and unequally distributed, with most practicing in urban regions. Unsafe and outdated methods like sharp curettage are frequently used. Medical management of second-trimester post-abortion care by midwives offers an advantage given the difficulty in providing surgical management in low-income settings and current health worker shortages. The study aims to assess the safety, effectiveness and acceptability of treatment of incomplete second-trimester abortion using misoprostol provided by midwives compared with physicians. METHODS: A randomized controlled equivalence trial implemented at eight hospitals and health centers in Central Uganda will include 1192 eligible women with incomplete abortion of uterine size > 12 weeks up to 18 weeks. Each participant will be randomly assigned to undergo a clinical assessment and treatment by either a midwife (intervention arm) or a physician (control arm). Enrolled participants will receive 400 μg misoprostol administered sublingually every 3 h up to five doses within 24 h at the health facility until a complete abortion is confirmed. Women who do not achieve complete abortion within 24 h will undergo surgical uterine evacuation. Pre discharge, participants will receive contraceptive counseling and information on what to expect in terms of side effects and signs of complications, with follow-up 14 days later to assess secondary outcomes. Analyses will be by intention to treat. Background characteristics and outcomes will be presented using descriptive statistics. Differences between groups will be analyzed using risk difference (95% confidence interval) and equivalence established if this lies between the predefined range of - 5% and + 5%. Chi-square tests will be used for comparison of outcome and t tests used to compare mean values. P ≤ 0.05 will be considered statistically significant. DISCUSSION: Our study will provide evidence to inform national and international policies, standard care guidelines and training program curricula on treatment of second-trimester incomplete abortion for improved access. TRIAL REGISTRATION: ClinicalTrials.gov, NCT03622073 . Registered on 9 August 2018.