Background: Poor male fecundity is of concern and warrants the identification of potential modifiable risk factors. Short and long sleep duration might be risk factors for poor male fecundity although evidence in this research field is inconsistent. Objectives: To investigate the association between sleep duration and biomarkers of male fecundity in young men. Materials and methods: We conducted a cross-sectional study of 1,055 young men from the Fetal Programming of Semen Quality (FEPOS) cohort, Denmark, 2017–2019. Sleep duration was obtained from an online survey answered by the participants prior to the clinical visit, where semen and blood samples were obtained, and testis volume was self-assessed using an Orchidometer. Percentage differences in semen characteristics, testes volume, and reproductive hormone levels were analysed according to sleep duration using multivariable negative binomial regression models. Sleep duration was dichotomised (recommended (6–9 h/night) versus deviant sleep) and visualised continuously as restricted cubic spline plots. Results: Deviation from recommended sleep duration was associated with higher high DNA stainability (HDS) of 5% (95% CI: −1%; 13%), higher testosterone of 3% (95% CI: 0%; 7%) and higher free androgen index (FAI) of 6% (95% CI: 0%; 13%). The spline plots overall supported these results, suggesting u-shaped associations between sleep duration and HDS, testosterone and FAI, a linear association between sleep duration and semen volume and sex hormone binding globulin (SHBG) and an inverse u-shaped association with normal morphology. Discussion: Information on sleep duration was obtained by self-report in broad categories with at least 3 h intervals. We were not able to investigate short or long sleep duration separately, since only few participants reported this. Conclusion: Sleep duration was associated with some biomarkers of fecundity in young men. Maintaining a recommended sleep duration may thus be beneficial for young men with regard to reproductive health.