Long-acting and permanent contraceptive methods (LAPM) are effective and economical methods for delaying or limiting pregnancies, however they are not widely used. The Kenya government is promoting the use of modern methods of family planning through various mechanisms. This study aimed to determine the prevalence and factors associated with the use of LAPM among married women of reproductive age in targeted rural sub-counties of Kilifi and Kisii counties, Kenya. Baseline and end line Data from a program implemented on improving Access to Quality Care and Extending and Strengthening Health Systems (AQCESS) in Kilifi and Kisii counties of Kenya were used. Multi-stage sampling was used to sample 1117 and 1873 women for the end line and baseline surveys, respectively. Descriptive analysis was used to explore the respondents' characteristics and use of LAPM on a self-weighted samples. Univariable and multivariable binary logistic regression models using svy command were used to assess factors associated with the use of LAPM. A total of 762 and 531 women for the baseline and end line survey, respectively were included in this study. The prevalence of use of LAPM for baseline and end line survey were 21.5% (95% CI: 18.7-24.6%) and 23.2% (95% CI: 19.6%-27.0%), p-value = 0.485. The use of LAPM in Kisii and Kilifi counties was higher than the national average in both surveys. The multivariable analysis for the end line survey showed having 3-5 number of children ever born (aOR = 2.04; 95% CI: 1.24-3.36) and future fertility preference to have another child (aOR = 0.50; 95% CI: 0.26-0.96) were significantly associated with odds of LAPM use. The baseline showed that having at least secondary education (aOR = 1.93; 95%CI: 1.04-3.60), joint decision making about woman's own health (aOR = 2.08; 95%CI: 1.36-3.17), and intention to have another child in future (aOR = 0.59; 95%CI: 0.40-0.89) were significantly associated with the use of LAPM. Future fertility preference to have another child was significantly associated with the use of LAPM in the two surveys. Continued health promotion and targeted media campaigns on the use of LAPM in rural areas with low socioeconomic status is needed in order to improve utilization of these methods. Programs involving men in decision making on partner's health including family planning in the rural areas should be encouraged.