Background: Emergency contraception (EC) is a method used to prevent the occurrence of pregnancy after unprotected intercourse. Unwanted pregnancy is a common problem among young unmarried women in Ethiopia where more than 60% of all pregnancies among adolescents is unwanted. Despite the availability this method, the prevalence of abortion is still high however, little is known about use of EC and factors influencing its use among girls attending higher education in Ethiopia. Objective: To assess magnitude and factors affecting emergency contraceptive use and prevalence of unwanted pregnancy among female students in Aksum University. Method: A cross-sectional quantitative study was done among 628 female under graduate students in Aksum University using structured self administered questionnaire. Multistage sampling technique was used to select participants. Data were cleaned and analyzed using SPSS version 21. Multivariate logistic regression analysis was done to identify independent predictors of EC and variables with p-value <0.05 considered as significant predictors. Result: A total of 617 students participated in this study. About quarter 147(23.8%) of the respondents ever had sexual intercourse and 29 (19.7%) where married, 26(26.5%) had sex had their sexual debut before 18 years. Fifty eight (39.5%) had been pregnant of whom 40(69%) were unwanted. Ever use of emergency contraceptive among the sexually active was 92 (62.6%). Respondents who visited religious place at least once a week were 3.76 times [AOR= 3.76; 95%CI, [2.482, 9.555], single 4.88 times [AOR= 4.88 95%; 1.937-12.288], respondents who have good knowledge on contraceptive 2.39 times [AOR=2.39 95% CI; 1.202, 4.743], study year 8.71 (AOR=8.71; 95% CI; 2.68, 28.8) more likely to use emergency contraceptive than their counterparts. Whereas those who did not discuss with their close friend on emergency contraceptive 63% [AOR= 0.37, 95%, CI; 0.193, 0.703] and those who never discussed on reproductive health issue with their family 42% [AOR= 0.58, 95%, CI0.321, 1.036] less likely to use emergency contraceptive than counter parts. Conclusions and recommendations: The prevalence of unwanted pregnancy is high while emergency contraceptive use among the sexually active students was low .This may put young girls at risk complication of unsafe abortion including premature death. There is a need to educate adolescents about EC use in averting unwanted pregnancy through creating and strengthening different clubs at schools.