Background Globally, early adolescents (10-14 years) represent 8% of the world population, and Africa accounts for 25% of them. Although a minority of early adolescents have initiated sexual intercourse, their sexual curiosity results in the exploration and understanding of sexuality. Early sexual intercourse may lead to sexually transmitted infections, HIV/AIDS, early pregnancy or fatherhood, and early marriage. Early sexual activity is associated with high rates of unplanned pregnancy, multiple sexual partners, and other forms of risky sexual behaviours. Understanding sexual activity among early adolescents can contribute to designing interventions that adequately address their needs. However, there is limited information about early adolescents' sexual activity and the social-ecological factors associated with their sexual experiences. This study aimed to determine the prevalence of sexual activity and the social-ecological factors associated with sexual experiences among early adolescents (12-14 years) in Rwanda. Methods We conducted a cross-sectional study among early adolescents (12-14 years) from four districts and 16 secondary schools between November and December 2020. A multistage sampling technique was used to select 56 participants from each school, including 28 males and females from grades one and two, who were randomly selected. We used an adapted version of the Illustrative Questionnaire for Interview - Surveys with Young People. Questions focused on nonpenetrative and penetrative sexual experiences in addition to sociodemographic and other social-ecological characteristics. Ethical clearance was obtained from the University of Rwanda and the University of the Witwatersrand, Johannesburg. Written parental or legal guardian consent and participants' assent were obtained. We conducted the data analysis in Stata 14.2 and used descriptive statistics (frequencies and proportions), bivariate and multivariate logistic regression analyses with 95% confidence intervals (CIs) and a significance level of p-value <0.05. Results The study included 811 participants, 55.1% of whom were aged 14, 30.5% were aged 13, and 14.4% were aged 12. Most participants (n=539, 73.5%) lived with both parents, and 48.8% (n=395) described the socioeconomic status of their households as well-off. Nearly 81% (n=658) of the participants indicated that they had experienced non-penetrative sex, and 53 of 759 participants (7%) reported that they had experienced penetrative sex. The social-ecological factors significantly associated with nonpenetrative sexual experiences were attending parties (AOR=6.8, 95% CI= 1.6-29.2), internet use (AOR=1.9, 95% CI= 1.1-3.3) (individual level), and their fathers’ low education (primary: AOR=2.6, 95% CI= 1.4-5.0; secondary: AOR=1.9, 95%CI: 1.0-3.8) (family level). Individual level factors such as male sex (AOR: 4.6, 95% CI= 1.8-12.4), alcohol consumption (AOR=3.5, 95% CI= 1.4-8.8), watching pornography (3-4 times: AOR=7.5, 95% CI= 1.6-34.9, ≥ five times: AOR= 5.1, 95% CI= 1.7-15.0), being a double orphan (AOR:17.8, 95% CI= 1.9-170.2), discussing sex matters often with one’s father (AOR=6.5, 95% CI= 1.8-23.2) (family and relationship level), and forced sexual intercourse (AOR=8.2, 95% CI= 2.7-25.4) (community level) were social-ecological factors associated with penetrative sexual experience. Conclusion Nonpenetrative sexual experience was common, with few participants reporting penetrative sexual experience. The social-ecological factors associated with sexual experiences among early adolescents are modifiable and can assist in planning healthy sexual interventions for this age group.