Abstract Background Women empowerment is recognized as a potential enabling factor to the utilization of health facilities during childbirth. However, the association between women empowerment and utilization of health facilities is poorly studied, especially in counties with high maternal mortality. Therefore, we investigated the association between women empowerment indices and the utilization of health facilities during childbirth in Sierra Leone. Methods We analyzed secondary data from the 2019 Sierra Leone Demographic and Health Survey (SLDHS). We included 5,997 married women who had given birth in the five years before the survey, and had been sampled for the women empowerment questionnaire. The study employed the gender roles framework developed by the Harvard Institute for International Development in the selection and classification of women empowerment indices, which include influencing, resource and decision-making factors. We conducted logistic regression analyses using SPSS version 25.0 complex samples package to determine the association between women empowerment indices and utilization of health facilities. Results The overall prevalence of health facility utilization during childbirth was 84.1% (5,042/5,997): 95% CI: 83.6 to 85.4. Among the influencer domain variables, women from the southern (aOR = 2.25, 95% CI: 1.34–3.78), northern (aOR = 1.69,95% CI: 1.01–2.82) and eastern regions (aOR = 3.71, 95% CI: 2.03–6.77) had higher odds of health facility utilization compared to women in the western region, while women in polygamous marriages (aOR = 0.82, 95% CI: 0.69–0.98) had lower odds of utilizing health facilities compared to their counterparts in monogamous marriages. Furthermore, women who had their first birth when they were less than 18 years, had higher odds of utilizing health facilities (aOR = 1.22, 95% CI: 1.02–1.45) compared to those who were 18 years and above. Among the resource domain variables, women with post-primary education (aOR = 1.58, 95% CI: 1.21–2.06) had higher odds of utilizing health facilities compared to their counterparts with no education and women who belonged to the richest wealth quintile (aOR = 2.42, 95% CI: 1.31–4.46) had higher odds of utilizing health facilities compared to their counterparts belonging in the poorest quintile. None of the variables in the decision making domain was significantly associated with health facility utilization. Conclusion These findings emphasize that, successful implementation of health facility utilization interventions should prioritize women empowerment with more pragmatic efforts. Policies and programme should aim at all women with more focus on those having lower education (primary and below), belonging to the poorest wealth quintile, give birth before reaching18 years and in polygamous marriages.