Terrestrial evapotranspiration (ET) is the second largest water flux in the global water cycle. It can be measured with different techniques; weighable lysimeters can provide very accurate measurements, and some very long-term time series exist. However, these lysimeter time series are affected by data gaps that must be filled to estimate actual ET totals and long-term trends. In this paper, we explore four different gap-filling methods: the potential ET-method, the ratio method, the FAO-based water balance method, and HYDRUS modeling. These gap-filling methods were evaluated for three time series of actual ET measured by lysimeters and meteorological data of three European sites. Separate evaluations were made for the five driest and five wettest April–October periods to investigate whether the performance of the gap-filling methods was affected by hydrological conditions. Series of random gaps were artificially created for the three time series, including gaps of four different lengths. Actual ET was estimated for these gaps with the gap-filling methods, which were evaluated based on RMSE and mean bias error. The results show that the ratio method outperformed other methods for gap filling of lysimeter data for Basel (Switzerland), whereas the HYDRUS method outperformed other methods for Rheindahlen (Germany). For Rietholzbach (Switzerland), the different methods performed very similarly, except that the FAO method gives slightly larger RMSEs. The gap-filling methods do not perform very differently for dry and wet conditions. The ratio method is recommended for filling smaller gaps, and the HYDRUS method is recommended for longer gaps of 30 d.