Setting: All public health facilities in Bonthe District, rural Sierra Leone. Objective: To compare, in the periods before and during the Ebola virus disease outbreak, 1) the submission and completeness of monthly human immunodeficiency virus (HIV) reports, and 2) the uptake of HIV testing and care for pregnant women and the general population. Design: A cross-sectional study using routine programme data. Results: Of the 627 HIV reports expected in each period, 406 (65%) were submitted in the pre-Ebola period and 376 (60%) during the Ebola outbreak (P = 0.08), of which respectively 318 (78%) and 335 (89%) had complete information (P < 0.001). In the pre-Ebola period, 5012 pregnant women underwent testing for HIV, of whom 25 were HIV-positive, compared to 4254 during the Ebola period, of whom 21 were HIV-positive (P < 0.001). Of those who were HIV-positive, respectively 14 (56%) and 21 (100%) received antiretroviral prophylaxis or antiretroviral therapy (ART) (P < 0.001). In the general population, 5770 persons underwent HIV testing pre-Ebola vs. 3095 in the Ebola period (P < 0.001); of those who tested positive for HIV, respectively 62% (33/53) and 81% (33/41) were started on ART (P = 0.06). Conclusion: There was suboptimal reporting on HIV/acquired immune-deficiency disease syndrome activities before and during the Ebola virus disease outbreak. HIV testing decreased during the Ebola outbreak, while the uptake of prevention of mother-to-child transmission and ART increased. Pre-emptive actions are needed to maintain the levels of HIV testing in any future outbreak.