As caesarean delivery rates continue to increase globally, so are the number of second-stage caesarean deliveries. Second-stage caesareans may carry additional risk of complications for both the mother and fetus owing to fetal head impaction into the maternal pelvis and manipulations required for delivery. So far, data on this procedure's outcomes from low resource countries are limited. To compare adverse maternal and perinatal outcomes between second-stage and first-stage of labour intrapartum primary caesarean deliveries over 12 months at a tertiary referral obstetric hospital in Kenya. In a hospital-based cohort study, 222 women with singleton, cephalic presenting fetuses at term gestation who had intrapartum primary caesarean delivery during active labour were recruited post-partum. Second-stage caesarean deliveries (73) were compared to 149 first-stage caesarean deliveries. The proportion of caesarean deliveries in the second-stage of labour was estimated and the adverse maternal and perinatal outcomes were compared. The study was conducted from August 2021 to July 2022 at the Moi Teaching and Referral Hospital, Eldoret. The proportion of second-stage caesarean deliveries among intrapartum primary caesarean deliveries was 4.3% [95% CI: 2.9% - 4.7%]. Compared to first-stage caesarean deliveries, second-stage caesarean deliveries had a significantly higher risk of adverse maternal outcomes (RR 3.272, 95% CI 2.28-4.71, P < 0.001), including intraoperative trauma, atony, blood transfusion, and a postoperative hospital stay of more than three days. Additionally, there was a higher risk of adverse perinatal outcomes (RR 2.748, 95% CI 2.45-4.50, P < 0.001), including increased risk of a 5-min APGAR ≤3, admission to NBU, and neonatal death. An increased risk of adverse maternal and perinatal outcomes is associated with primary second-stage caesarean deliveries compared to primary first-stage caesarean deliveries.