Background Modern Contraceptive Methods (MCM) use is among the interventions preventing unplanned pregnancies and unsafe abortions globally. Nevertheless, MCM uptake is still low. We aimed at determining factors influencing contraceptive uptake among women of reproductive age 15 to 49 years, in Kenya. Methods We used secondary data collected by Performance, monitoring for Action (PMA). PMA used cross sectional multi-stage cluster survey design and collected the data between November and December 2019. The study was approved by NACOSTI/202974 and KNERC KNH/ERC/R/192. Results The study obtained a sample size of 9477 women of reproductive age (WRA) from 11 counties in Kenya. Both descriptive and inferential statistical analysis with a P value of 0.05 was done using Stata 16.1. The prevalence of modern contraceptives uptake was 43.2% among all WRA, which was lower among rural dwellers 41.4% (95% CI 39.62, 43.17) as compared to urban dwellers 47.5 (95% CI 44.39,50.55). More than half (53.4%) of the married women were using a modern contraceptive, while only about two in every 10 of the unmarried were using a modern contraceptive. Women affiliated with the Islam religion were less likely to use modern contraceptive (aPOR 0.6, 95% CI 0.42, 0.89 p=0.010) as compared to the Catholics. Family planning (FP) services were found to be lower (aPOR 0.535(95% CI 0.29,0.98 p=0.043) in National Hospital Insurance Fund (NHIF)-covered facilities than in non-NHIF-covered ones. Adolescent FP service provision and prescription was significant (aPOR 4.0 95% CI; 1.05,15.41, p=0.42). Conclusion Low uptake for MCM is influenced by sociodemographic factors and Health system factors. Efforts to increase MCM uptake should focus on rural residents, unmarried women, Islamic religion women and accreditation of NHIF services in all facilities.