Summary The well‐established effects of evening preference on diminished well‐being and poorer mental health are usually explained in terms of common genetic bases of eveningness and negative emotionality and/or the discrepancy between biological and social clocks, experienced far more frequently by the Evening‐types. However, recent studies provide evidence for the negative stereotyping of evening chronotypes which may lead to unexpectedly pronounced social stigma and its consequences. The present article provides a seminal empirical analysis of the role of perceived chronotype‐related discrimination in the association between morningness‐eveningness and both positive affect and negative affect. The study was conducted on a gender‐balanced sample of 768 individuals aged between 18 and 56 years who filled measures of morningness‐eveningness, positive and negative affect, as well as a modified version of the Perceived Devaluation Discrimination scale, tentatively labeled Perceived Chronotype‐Related Discrimination scale ( https://osf.io/urs8x/ ), developed to measure the sense of chronotype‐based discrimination. Conducted analyses provided evidence for a positive association between eveningness and perceived discrimination. Moreover, perceived discrimination partly mediated the associations between morningness‐eveningness and both positive affect and negative affect, explaining 18% and 29% of these effects, respectively. Hence, our results provide initial evidence for yet another mechanism through which chronotype may impact emotional functioning, namely the experience of chronotype‐based stigmatisation.