BACKGROUND: Dental caries is an alarming health problem worldwide and the leading cause of oral infection among children and adolescents. This study aimed to determine the prevalence of dental caries and its associated factors among secondary school students in Kigali, Rwanda. METHODS: A cross-sectional study was conducted among 646 secondary school students aged 12 to 25 in Kigali. Being a student in a secondary school in the city of Kigali was the criteria to participate in the study. Data on dental caries were collected with a structured questionnaire adapted from the World Health Organization. A proportional random sampling was used to select secondary schools. Then a systematic sampling was used to recruit the participants. The data were analyzed with SPSS version 25. Proportions of dental caries and the mean decayed missing and filled teeth index (DMFT) were computed. Bivariate and Poisson regression analyses were used to test the factors associated with dental caries. RESULTS: The average age of study participants was 16 years. Almost half of the study participants were female (50.5%) and were from an urban place of residence (50%). The overall prevalence of dental caries was 61.1% with a mean decayed missing and filled teeth index of 3.3 (SD = 3.9). Notably, 5.1% of children had missing teeth, however, only 1.7% had filled teeth. The lower molars were the most affected by tooth decay 38.7%. Females were 1.5 times more likely to develop dental caries (AOR = 1.5, CI:1.4-1.6, P = 0.001) compared to males. Children from rural areas had 1.1 times higher odds of dental caries (AOR = 1.1, CI:1.0-1.3, P <
0.001) compared to their urban counterparts. Not using fluoridated toothpaste twice a day or more was 1.2 times more likely to develop dental caries than those who use it regularly (AOR = 1.2, CI:1.1-1.3, P <
0.001). Those visiting a dentist regularly were estimated to have 30% lower odds of dental caries (AOR:0.7, CI:0.6-0.8, P <
0.001). Moreover, being young (12 - 14 years) and coming from a poor family was associated with a 40% and 20% lower likelihood of dental caries compared to their counterparts. CONCLUSION: The high prevalence of dental caries among secondary school students in Kigali was linked to factors such as infrequent dental visits, coming from low-income families, residing in rural areas, and being female.