Even if the cesarean section is one of the most common and lifesaving surgical procedure, there is an increasing concern on the needless cesarean section that causes maternal and perinatal morbidity. In Ethiopia, insufficient studies are conducted about the current rate of the cesarean delivery. As a result, this study aimed to assess the magnitude of the cesarean section and its associated factors among mothers who gave birth in Nigist Eleni Mohammed Memorial Referral Hospital Hossana Town, Southern Ethiopia. An institution-based cross-sectional study was employed from May 1, 2018, to August 30, 2018 among a total of 3360 deliveries within four months. Data were collected using an interviewer-administered questionnaireand chart review checklist from 320 women who delivered at Nigist Eleni Mohammed Memorial Referral Hospital. The data were collected from every four women until the desired sample size was achieved. After checking visually for completeness, the collected data were entered into EpiData version 3.1 and analyzed using SPSS version 20.0. Descriptive statistics such as frequency, mean and standard deviation were used to describe the characteristics of the participants. Bivariate and multivariable logistic regression was applied to identify factors associated with cesarean delivery. Statistical significance was declared at P < 0.05. Among a total of 1120 women delivered during the study period, a total of 315 women were involved in this study making a response rate of 98.4%. Of the participants, 24.1% (95%CI: 19.3%, 28.8%) delivered through caesarean section. Age less than twenty-five years (AOR = 0.36, 95% CI = 0.14, 0.91), attend primary education (AOR = 0.33, 95% CI: 0.14, 0.78), secondary education (AOR = 0.36, 95% CI: 0.15, 0.85), gravida to IV (AOR = 3.99, 95% CI: 1.23, 12.98) and labor not attended using partograph (AOR = 4.04 95% CI: 2.08, 7.82) were independently associated with cesarean delivery. In general, one-quarter of women delivered through the cesarean section which is higher than the WHO recommendation. Factors such as high maternal age, not attending formal education, multigravida, and not using partograph to monitor labor were independent factors associated with cesarean delivery. Thus, labor progress must be followed using partograph and all mothers should be encouraged to deliver through the natural route. Furthermore, obstetric care providers need not rush into cesarean section except for minimal episode of fetal or maternal complication and they should adhere to the clinical and WHO guidelines.