An estimated 80% of the population in developing countries is dependent on traditional medicine for their health needs, including use during pregnancy despite limited knowledge of potential side effects including teratogenicity. Controlling use of traditional medicines during pregnancy requires understanding the driving factors. This study aimed at determining the health system factors that influence traditional herbal medicine use during pregnancy in a Ugandan setting. A cross-sectional study was conducted among 315 post-partum women obtained by random sampling from post-natal clinics of health facilities in Mpigi District after informed consent. We carried out concurrent triangulation by conducting two focused group discussions of 10 post-natal mothers each, and four Key informant interviews. Quantitative Data analysis involved descriptive statistics and logistic regression analysis. Qualitative data was analyzed by thematic content analysis and presented as narratives. Prevalence of herbal medicine use during pregnancy was 79% (95% Confidence Interval (CI) 68.1% - 86.9%), mainly consumed through oral route (96%). Costly health care adjusted Prevalence Ratio (aPR) 1.61 (95% CI 1.02-2.53), p-value 0.042, and presence and influence of Traditional Birth Attendants aPR 1.21(95% CI 1.05-1.41), p-value 0.011 were significantly associated with use of traditional herbal medicines during pregnancy. Use of traditional herbal medicines is driven by the high costs of quality health care and influence from Traditional Birth Attendants. Innovations in health financing should be promoted and Traditional Birth Attendants should be sensitized and incorporated in the mainstream health care system as community referral agents.