Background: The role of chronotype, the individual timing of sleep/activity, has been studied in relation to depressive and anxiety disorders. A cross-sectional association between a depressive episode and evening-type has been identified. However, until now the predicting capacity of chronotype concerning persistence of psychiatric disorders remains unclear. Our aim is to examine whether a later chronotype in patients with a depressive and/or anxiety disorder can serve as a predictor of a persistent course. Methods: A subsample of patients with a depressive and/or anxiety disorder diagnosis and chronotype data of the longitudinal Netherlands Study of Depression and Anxiety (NESDA) was used. Diagnosis of depressive and anxiety disorders (1-month DSM-IV based diagnosis) were determined at baseline (n = 505). From this group persistence was determined at 2-year (FU2) (persistent course: n = 248, non-persistent course: n = 208) and 4-year follow-up (FU4) (persistent course: n = 151, non-persistent course: n = 264). Chronotype was assessed at baseline with the Munich Chronotype Questionnaire. Results: A later chronotype did not predict a persistent course of depressive and/or anxiety disorder at FU2 (OR (95% CI) = 0.99 (0.83–1.19), P = 0.92) or at FU4 (OR (95% CI) = 0.94 (0.77–1.15), P = 0.57). Limitations: Persistence was defined as having a diagnosis of depressive and/or anxiety disorder at the two-year and four-year follow-up, patients may have remitted and relapsed between assessments. Conclusion: Chronotype, measured as actual sleep timing, of patients with a depressive or anxiety disorder did not predict a persistent course which suggests it might be unsuitable as predictive tool in clinical settings.