Participation in microcredit programs has so far received widespread research and policy attention in the context of health and empowerment among Bangladeshi women. However, not much is known regarding the relationship between participation in microcredit programs and healthcare autonomy (HA) among women. In the present study, we analyzed two nationally representative surveys (Bangladesh Demographic and Health Survey 2004 and 2014), to assess the relationships between MC membership and HA among adult women (n = 29163), while adjusting for various sociodemographic correlates. Self-reported healthcare decision-making autonomy was assessed by asking whether or not the participant had final say on her healthcare. The findings revealed that between 2004 (20.9%, 95%CI = 19.8, 22.0) and 2014 (14.1%, 95%CI = 13.3, 15.0), the proportion of women reporting HA decreased significantly, despite considerable improvements across several socioeconomic indices, including higher education enrollment and labor market participation. Between 2004 and 2014, the percentage of microcredit borrowers decreased for Grameen (18.9% vs. 10.7%) and BRAC (7.9% vs. 7.4%), while it increased for BRDB (0.9% vs. 7.0%). A multivariate regression analysis revealed that Grameen Bank membership was positively associated with reporting HA in both male- (OR = 1.16, 95%CI = 1.09, 1.23) and female-headed households (OR = 1.44, 95%CI = 1.13, 1.85). A positive association between microcredit membership and HA was also observed for BRAC (OR = 1.33, 95%CI = 1.20, 1.47) and BRDB (OR = 1.18, 95%CI = 1.09, 1.29), but in the male-headed households only. Further analysis indicated that membership with Grameen bank was the most important predictor of HA, followed by BRAC, BRDB, and ASA, with the degree of importance varying substantially between male- and female-headed households. In conclusion, these findings suggest the potential of microcredit programs to promote healthcare autonomy among Bangladeshi women and provide insights for further research, as to why certain programs are more effective than others.