Background Studies have shown that affordable health insurance can influence healthcare visits and increase the choice of medication uptake in sub-Saharan Africa. However, there is a need to document the influence of health insurance coverage and modern contraceptive use in order to encourage its uptake. Thus, this study examined the influence of health insurance coverage on modern contraceptive use among sexually active women in Nigeria. Methods The secondary dataset utilised in this study were derived from the 2018 Nigeria Demographic and Health Survey (NDHS). Data analyses were restricted to 24,280 women of reproductive age 15–49 years who were sexually active in the survey dataset. Weighted bivariate and multivariable logistic regression models were used to examine the influence of health insurance coverage on modern contraceptive use while controlling for possible confounders. A Significant level of alpha was determined at p < 0.05 using STATA 16.0. Results The prevalence of health insurance coverage and modern contraceptive use among sexually active women in Nigeria were 25.47% and 13.82%, respectively. About 1 out of every 4 sexually active women covered by health insurance were using a modern contraceptive, while 86.50% of the women not covered by health insurance were not using any modern contraceptive method. After adjusting for socio-demographic characteristics, the odds of using any modern contraceptive were significantly higher for sexually active women who were covered by any health insurance [aOR = 1.28; 95% (CI = 1.01–1.62)] compared to sexually active women not covered by health insurance in Nigeria. Conclusion The study demonstrated that health insurance coverage is a significant driver of health service utilization, including modern contraceptive use. Health insurance benefits are recommended to be expanded to cover a broader spectrum of family planning services in Nigeria. More research is required to understand the influence of different health insurance schemes and the use of modern family planning methods in Nigeria.