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Introduction: The low use of modern contraceptive methods by young girls is a real public health problem in sub-Saharan Africa, especially among young female students living in rural areas. The purpose of this study was to analyze the factors associated with contraceptive use among young female students in rural Guinea. Method: This was an analytical cross-sectional study including 607 students from 10 secondary schools in the rural district of Kankan, Guinea. Results: A total of 607 female students were interviewed and included in this study. They had an average age of 17.3 ± 1.7 years, 50.9% were in junior high school, and 49.1% were in high school. During our survey period, 67.7% of the girls reported being sexually active, while only 24.4% were on modern contraception. In the bivariate analysis, factors such as age, religion, school level, having heard of contraception, and having had sexual intercourse were statistically associated with contraceptive use. In the multivariate analysis, factors such as age (OR = 2.1; CI = 1.1–3.8), religion (OR = 5.1; CI = 2.8–9.5), and having had sexual intercourse (OR = 2.2; CI = 1.4–3.5) remained statistically associated with the use of contraceptive methods among young female students. Conclusion: Our study highlights the need to increase awareness of, and access to, contraceptive methods in schools in order to improve contraceptive practice and, in turn, to reduce the frequency of unwanted and early pregnancies among young female students in rural areas of Guinea.