Background: Adolescent pregnancy carries a high risk of severe health issues for both the mother and the newborn. Worldwide, 21 million adolescents give birth every year, with high percentages in Latin America. Most of the risk factors are met in indigenous communities, which is an underrepresented and poorly studied population. We aimed to assess the determinants of adolescent pregnancy in indigenous communities from the Peruvian central jungle. Methods: Through a case–control study, female adolescents aged 13 to 19 years old from seven indigenous communities of the Peruvian central jungle were interviewed. Adolescents with (cases) and with no (controls) pregnancy history, such as current pregnancy, children and abortion, fulfilled our eligible criteria. Our instrument explored: sociodemographic, adolescent and family characteristics, as well as perceptions of adolescent pregnancy. We performed a penalized maximum likelihood logistic regression analysis to obtain Odds Ratios (OR) and their 95% confidence intervals (95% CI). Results: We enrolled 34 cases and 107 controls. Overall, 53.9% were 15 to 19 years old. We found a significant association of being 15–19 years old (OR = 6.88, 95% CI 2.38–19.86, p < 0.0001) and an elementary school level of instruction (OR = 5.59, 95% CI 1.95–16.06, p = 0.001) with the risk of adolescent pregnancy. A marginal statistical significance between having five to six siblings and adolescent pregnancy was also reported (OR = 2.70, 95% CI 0.85–8.61, p = 0.094). Furthermore, adolescents with sexual and reproductive health communication with parents had a lower risk of adolescent pregnancy (OR = 0.17, 95% CI 0.06–0.47, p = 0.001). Conclusion: Our results suggest that public health and educational efforts should be age-specific focused within indigenous communities of the Peruvian central jungle, encouraging parents to talk about sexual and reproductive health topics with adolescents.