Chronotype is an individual difference trait that is closely linked to biological variables. Usually, men and women differ in their chronotype with men being more evening oriented than women. The aim of the study was to assess gender differences in chronotype based on a systematic review and meta-analysis. In addition, many recent studies do not report gender differences any more although researchers collected data on men and women. This motivated us to contact many researchers directly to obtain and use these additional data. We included 164 studies giving 201 effect size measures in a data set, which only included the most commonly used questionnaires (MEQ, rMEQ and CSM) totaling 186,289 participants in total, of which 75,622 were men and 110,667 were women. We calculated an effect size of the standardized mean difference of -0.072 (95% CI from -0.062 to -0.082) in the fixed effects and of -0.066 (95% CI from -0.043 to- 0.089) in the random effects model. Men were on average more evening oriented than women. Type of questionnaire did not influence the standardized mean difference in chronotype between genders. Mean age, standard deviation of age and publication year (p ≤ 0.05) were found to have significant effects on the standardized mean difference in chronotype between genders. The standardized mean difference in chronotype between genders is predicted to change from negative to positive with increasing mean age (young women were more morning orientated than young men, but older women were less morning orientated than older men). This suggests that the differences between men and women diminish with time. The standardized mean difference in chronotype between genders is decreasing with increasing publication year, as well as with high variation in age of the samples. Abbreviations: CSM: Composite Scale of Morningness (Smith et al. 1989); MEQ: Morningness-Eveningness Questionnaire (Horne and Ostberg, 1976); rMEQ: reduced Morningness-Eveningness Questionnaire (Adan & Almiral, 1991); SMD: standardized mean difference (measure of effect size).