Masturbation is a common sexual practice in men, and saliva is often used as a lubricant during masturbation by men who have sex with men. However, the role of saliva use during masturbation in the transmission of chlamydia is still unclear. We developed population-level, susceptible-infected-susceptible compartmental models to explore the role of saliva use during masturbation on the transmission of chlamydia at multiple anatomical sites. In this study, we simulated both solo masturbation and mutual masturbation. Our baseline model did not include masturbation but included transmission routes (anal sex, oral-penile sex, rimming, kissing and sequential sexual practices) we have previously validated (model 1). We added masturbation to model 1 to develop the second model (model 2). We calibrated the model to five clinical datasets separately to assess the effects of masturbation on the prevalence of site-specific infection. The inclusion of masturbation (model 2) significantly worsened the ability of the models to replicate the prevalence of C. trachomatis. Using model 2 and the five data sets, we estimated that saliva use during masturbation was responsible for between 3.9% [95% confidence interval (CI) 2.0–6.8] and 6.2% (95% CI 3.8–10.5) of incident chlamydia cases at all sites. Our models suggest that saliva use during masturbation is unlikely to play a major role in chlamydia transmission between men, and even if it does have a role, about one in seven cases of urethral chlamydia might arise from masturbation.