Estimating evapotranspiration in hilly watersheds is paramount for managing water resources, especially in semi-arid regions. Eddy covariance (EC) technique allows continuous measurements of latent heat flux LE. However, time series of EC measurements often experience large portions of missing data, because of instrumental dysfunctions or quality filtering. Existing gap-filling methods are questionable over hilly crop fields, because of changes in airflow inclination and subsequent aerodynamic properties. We evaluated the performances of different gap-filling methods before and after tailoring to conditions of hilly crop fields. The tailoring consisted of beforehand splitting the LE time series on the basis of upslope and downslope winds. The experiment was setup within an agricultural hilly watershed in northeastern Tunisia. EC measurements were collected throughout the growth cycle of three wheat crops, two of them located in adjacent fields on opposite hillslopes, and the third one located in a flat field. We considered four gap-filling methods: the REddyProc method, the linear regression between LE and net radiation Rn, the multi-linear regression of LE against the other energy fluxes, and the use of evaporative fraction EF. Regardless of method, the splitting of the LE time series did not impact the gap filling rate, and it might improve the accuracies on LE retrievals in some cases. Regardless of method, the obtained accuracies on LE estimates after gap filling were close to instrumental accuracies, and were comparable to those reported in previous studies over flat and mountainous terrains. Overall, REddyProc was the most appropriate method, for both gap filling rate and retrieval accuracy. Thus, it seems possible to conduct gap-filling for LE time series collected over hilly crop fields, provided the LE time series are beforehand split on the basis of upslope / downslope winds. Future works should address consecutive vegetation growth cycles for a larger panel of conditions in terms of climate, vegetation and water status.