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Background: In 205 health facilities, mother-to-child transmission (MTCT) of human immunodeficiency virus (HIV) rates were reduced from 7.4% to 2.1% between 2017 and 2020, respectively. Aim: To determine characteristics that potentially correlate to the change in MTCT rates between two time points. Setting: Study was conducted in Kenya, semi-urban and rural areas. Methods: A retrospective, cross-sectional, exploratory analysis of programme implementation at two points in time (2017 and 2020). Between 2017 and 2020, we compared over 170 mother–infant pairs where MTCT occurred to over 6000 mother–infant pairs where MTCT did not occur through the following factors: (1) location of health facilities, (2) mother and infant characteristics, (3) access to antiretroviral therapy (ART), and (4) viral load suppression. Bivariate and multivariable logistic regression models were used to identify factors associated with MTCT. Results: Factors significantly associated with reduced MTCT rates were time points, mother’s age, infant age at first test, proportions of mothers receiving ART, and maternal viral load. When restricting the analysis to the sub-counties contributing data at both time points, the results were similar; however, counties’ location became significant in the updated model, as did the interaction term for mother and infant receipt of antiretrovirals (odds ratio [OR]: 0.228; p = 0.04). Conclusion: What changed between 2017 and 2020 is a higher proportion of pregnant women living with HIV received ART. Also, unlike in 2017, in 2020, tenofovir disoproxil fumarate was the backbone of the ART regimen for the prevention of MTCT. Contribution: The findings can potentially inform efforts on elimination of mother-to-child transmission of HIV.