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Indigenous people have poorer reproductive health outcomes than the general population and face considerable barriers in accessing adequate health services. Indigenous women have high rates of unintended pregnancy and may face increased risks for morbidity and mortality related to unsafe abortion. 47% of all pregnancies in Rwanda are unintended with an annual rate of 114 unintended pregnancies per 1,000 women. The study determined the use of emergency contraceptive and factors influencing their use among female students of Mount Kenya University. A descriptive cross-sectional study was undertaken. The target population was 824 female students of MKU Kigali campus. 263 female students constituted the random sample. A self-administered questionnaire was used to collect data. The findings revealed that 50.7% of respondents faced contraceptive risks; only 30.6% of them used EC after facing an EC risk. The most used FP methods were pills (97, 9%). The factors contributing to non use of EC among MKU female students, includeLack of knowledge on EC (86.2), Fear of side effects (58.7%), 43.1% of respondents do not know where to find them. The EC use was reported that is against religion beliefs (22%). The culture does not support the use of EC (93.2%). The majority of the respondent were female students (86.9%) aged between 21 and 35years old, 90.1% were Christians 62.7% are living in urban area, 59.7% were single during the study and 31.2% of students were married. It has also been found that58.6% of respondents have not been pregnant yet and 34.6 % had 1 to 2 pregnancies. The training on EC should be organized for students and Indigenous population on sexual and reproductive health, and use of EC to increase awareness and use of EC. An advocacy should be done on emergency contraceptive pills at school to increase their accessibility in case of need.