Abstract Background Emergency contraception (EC) can significantly reduce the rate of unintended pregnancies and unsafe abortions especially in sub-Saharan Africa. Despite the increasing awareness of EC among educated young women in Nigeria, the rate of utilisation remains low. This study therefore explores the main barriers to the use of EC among female university students by analysing their knowledge of emergency contraception, methods ever used, perceived efficacy, and its acceptability. Methods This paper brings together the findings from several focus groups ( N = 5) and in-depth interviews ( N = 20) conducted amongst unmarried female undergraduate students in two Nigerian universities. Results Participants considered the use of condom and abstinence as the most effective methods of preventing unplanned pregnancy. However, many participants were misinformed about emergency contraception. Generally, participants relied on unconventional and unproven ECs; Ampiclox, “Alabukun”, salt water solution, and lime and potash and perceived them to be effective in preventing unplanned pregnancies. Furthermore, respondents’ narratives about methods of preventing unwanted pregnancies revealed that inadequate information on emergency contraception, reliance on unproven crude contraceptive methods, and misconception about modern contraception constitute barriers to the use of emergency contraception. Conclusions The findings suggested that female university students are misinformed about emergency contraception and their reliance on unproven ECs constitutes a barrier to the use of approved EC methods. These barriers have serious implications for prevention of unplanned pregnancies in the cohort. Behavioural interventions targeting the use of unproven emergency contraceptive methods and misperceptions about ECs would be crucial for this cohort in Nigeria.