Lakes are considered the second largest natural source of atmospheric methane (CH4). However, current estimates are still uncertain and do not account for diel variability of CH4 emissions. In this study, we performed high-resolution measurements of CH4 flux from several lakes, using an automated and sensor-based flux measurement approach (in total 4,580 measurements), and demonstrated a clear and consistent diel lake CH4 flux pattern during stratification and mixing periods. The maximum of CH4 flux were always noted between 10:00 and 16:00, whereas lower CH4 fluxes typically occurred during the nighttime (00:00–04:00). Regardless of the lake, CH4 emissions were on an average 2.4 higher during the day compared to the nighttime. Fluxes were higher during daytime on nearly 80% of the days. Accordingly, estimates and extrapolations based on daytime measurements only most likely result in overestimated fluxes, and consideration of diel variability is critical to properly assess the total lake CH4 flux, representing a key component of the global CH4 budget. Hence, based on a combination of our data and additional literature information considering diel variability across latitudes, we discuss ways to derive a diel variability correction factor for previous measurements made during daytime only.