The N'Zérékoré region has 6 health districts with a total population of 1,696,807 in 2015 [1]. HIV prevalence is 1.6% in Guinea, with 120,000 people including 65,000 women [2]. In Guinea during the Ebola virus disease epidemic, the N'Zérékoré region was the most affected, leading to dysfunctional health services. The aim of this study was to assess the impact of the Ebola epidemic on HIV PMTCT. It covered a 4-year period and focused on HIV-positive pregnant women and their children in 19 health centers. We found a prevalence rate of 0.88% and an acceptance rate of 44.03%. Housewives accounted for 64%. The ARV treatment completion rate fell from 54.95% to 23.23%. The number of patients lost to follow-up increased during the Ebola epidemic. However, the rate of assisted deliveries fell from 94.87% to 69.17% p = 8.126e-06. Similarly, the number of children protected fell from 50.55% to 16.67%. HIV PMTCT has been negatively impacted, as evidenced by a drop in the number of assisted deliveries, an increase in the number of lost to follow-up, break-ups, etc., and a decrease in the number of children protected.