Maternal morbidity and mortality has remained a major public health concern worldwide. Basic emergency obstetric care is the primary intervention to prevent obstetric complications and maternal death. Episiotomy is one of the basic obstetrical procedures used to facilitate vaginal delivery, shorten the second stage of labor and prevent complications. However, there is a paucity of evidence on the prevalence and factors associated with episiotomy among women who gave birth in eastern Ethiopia. This study aimed to determine the prevalence of episiotomy and its associated factors among women who gave birth at public health facilities in Jigjiga town, eastern Ethiopia. A facility-based cross-sectional study was conducted among women who gave birth vaginally from May 1 to June 30, 2022. A total of 422 study participants were recruited using systematic random sampling. Data were collected using structured questionnaires through a face-to-face interview supported with standard observational checklist and reviewing medical records. A logistic regression analysis was carried out to examine the association between explanatory variables and episiotomy. An adjusted odds ratio (AOR) at a 95% confidence interval (CI) at a P-value <0.05 was used to declare significant association. The prevalence of episiotomy among women was 52.6% (95% CI: 47.8%, 57.0%). Obstetric complications during current pregnancy (AOR:3.92, 95% CI: 1.59, 9.68), birth weight ≥4000 gm (AOR: 4.30, 95% CI: 1.53, 12.04), induction of labor (AOR: 3.10, 95% CI: 1.62, 5.93), meconium-stained amniotic fluid (AOR:2.10, 95% CI: 1.14, 3.88), duration of the second stage of labor ≥90 minutes (AOR:3.09, 95% CI: 1.53, 6.23), instrumental delivery (AOR: 2.69, 95%, CI: 1.39, 5.19), and female genital mutilation (AOR: 2.91, 95% CI: 1.83, 4.64) were factors significantly associated with episiotomy. Slightly more than half of the women who gave birth at public health facilities in the study area underwent episiotomies. In addition to the common obstetric factors, having a female genital mutilation scar increased the risk of women's experiencing episiotomies. Therefore, intervention should be tailored to address the identified obstetric risk factors and avoid female genital mutilation in the community to reduce women's experiences of episiotomies in the future.