Cross-generational sexual relationships are a major route of transmitting HIV and STI between older and younger generations. However, previous research has focused mainly on the young women in these relationships. This study examined the characteristics of men engaging in non-marital sexual relationships with girls aged 15–19 in Nigeria. The data were drawn from the 2013 Nigeria Demographic and Health Survey, and the analysis was restricted to a sub-sample of 7557 men aged 30–49 who were sexually active in the 12 months prior to the survey. Data analysis was carried out using frequency distributions, chi-squared tests of association and binary logistic regression. It was found that 9.5% of men aged 30–49 reported engaging in cross-generational sexual relationships. Also, being older (OR = 0.35), married (OR = 0.37), having secondary or higher education (OR = 0.70; 0.59) and having sexual debut between ages 18 and 30 (OR = 0.73) were associated with a lower likelihood of having cross-generational sexual relationships. However, Muslim men (OR = 2.10), men from Igbo (OR = 1.90), Hausa/Fulani (OR = 8.47) and Northern and Southern minority tribes (OR = 4.73; 2.49), men living in rural areas (OR = 1.34), men who were over the age of 30 at sexual debut (OR = 2.67) and those with 2–4 and 5 or more lifetime sexual partners (OR = 1.43; 1.58) were significantly more likely to engage in cross-generational sexual relationships. Addressing the challenges of cross-generational sexual relationships can be an effective strategy to reduce the menace of HIV and STI transmission. Men who have low education, those aged 30–34 years, those who initiated sex at an older age, rural dwellers and those who have had several lifetime sexual partners need to be targeted while designing and implementing programmes and policies to reduce cross-generational sexual relationships in Nigeria. These interventions must also take into account the religious and cultural attitudes towards cross-generational sexual relationships, and further investigations should identify men’s motives for engaging in the practice.