Background Exposure to workplace gender-based violence (GBV) can affect women's mental and physical health and work productivity in higher educational settings. Therefore, this study aimed to examine the prevalence of GBV (workplace incivility, bullying, sexual harassment), and associated factors among Nigerian university women. Methods The study was an institutional-based cross-sectional survey. The multi-stage sampling technique was used to select 339 female staff from public and private universities in Enugu, south-east Nigeria. Data was collected using the Workplace Incivility Scale (WIS), Modified Workplace Incivility Scale (MWIS), Negative Acts Questionnaire-Revised (NAQ-R), and Sexual Experiences Questionnaire (SEQ). Descriptive statistics, independent samples t-test, Pearson’s Chi-square test, univariate ANOVA, bivariate, and multivariable logistic regression analyses were conducted at 0.05 level of significance. Results The prevalence of workplace incivility, bullying, and sexual harassment (SH) was 63.8%, 53.5%, and 40.5%. The 12-month experience of the supervisor, coworker, and instigated incivilities was 67.4%, 58.8%, and 52.8%, respectively. Also, 47.5% of the participants initiated personal bullying, 62.5% experienced work-related bullying, and 42.2% experienced physical bullying. The 12-month experience of gender harassment, unwanted sexual attention, and sexual coercion were 36.5%, 25.6%, and 26.6%, respectively. Being aged 35–49 years (AOR 0.15; 95% CI (0.06, 0.40), and ≥ 50 years (AOR 0.04; 95% CI (0.01, 0.14) were associated with workplace incivility among female staff. Having a temporary appointment (AOR 7.79, 95% CI (2.26, 26.91) and casual/contract employment status (AOR 29.93, 95% CI (4.57, 192.2) were reported to be associated with workplace bullying. Having a doctoral degree (AOR 3.57, 95% CI (1.24, 10.34), temporary appointment (AOR 91.26, 95% CI (14.27, 583.4) and casual/contract employment status (AOR 73.81, 95% CI (7.26, 750.78) were associated with workplace SH. Conclusions The prevalence of GBV was high. There is an urgent need for workplace interventions to eliminate different forms of GBV and address associated factors to reduce the adverse mental, physical, and social health outcomes among university women.