Background <p>Masturbation is a common practice across various demographics worldwide. However, its prevalence among the general population in Nigeria remains unknown. This study investigates the prevalence of self- and mutual masturbation and their associated factors among sexually active Nigerians.</p> Methods <p>Data were obtained from the Sexual Behaviour and HPV Infection in Nigerians in Ibadan cross-sectional study, including males and females aged 18–45 years. After obtaining consent, participants were asked during face-to-face interviews whether they had ever touched their genitals or inserted fingers into the vagina or anus for sexual pleasure (self-masturbation) or whether they and their sexual partners had ever touched each other’s genitals by hand for sexual pleasure (mutual masturbation). The prevalence of self- and mutual masturbation was reported using percentages, while their associations with participants’ demographic, lifestyle, and biological characteristics were examined using chi-square tests. Poisson regression with robust variance was performed to identify associated factors. Statistical significance was set at <i>p</i> &lt; 0.05.</p> Results <p>Mutual masturbation (83.7%) was more common than self-masturbation (64.9%) among participants. The prevalence of self-masturbation was significantly higher among males than females (69.9% vs. 62.4%, <i>p</i> = 0.022), while mutual masturbation was significantly higher among females than males (86.6% vs. 78.1%, <i>p</i> = 0.001). Occupation, smartphone ownership, and alcohol consumption were significantly associated with self-masturbation, while ethnicity, location, number of penile-vaginal sex partners, and receiving oral sex were associated with mutual masturbation.</p> Conclusion <p>Self- and mutual masturbation are highly prevalent among sexually active Nigerians, with distinct factors influencing each behaviour.</p>