Fully convolutional neural networks (FCN) are successfully used for the automated pixel-wise classification of aerial images and possibly additional data. However, they require many labelled training samples to perform well. One approach addressing this issue is semi-supervised domain adaptation (SSDA). Here, labelled training samples from a source domain and unlabelled samples from a target domain are used jointly to obtain a target domain classifier, without requiring any labelled samples from the target domain. In this paper, a two-step approach for SSDA is proposed. The first step corresponds to a supervised training on the source domain, making use of strong data augmentation to increase the initial performance on the target domain. Secondly, the model is adapted by entropy minimization using a novel weighting strategy. The approach is evaluated on the basis of five domains, corresponding to five cities. Several training variants and adaptation scenarios are tested, indicating that proper data augmentation can already improve the initial target domain performance significantly resulting in an average overall accuracy of 77.5%. The weighted entropy minimization improves the overall accuracy on the target domains in 19 out of 20 scenarios on average by 1.8%. In all experiments a novel FCN architecture is used that yields results comparable to those of the best-performing models on the ISPRS labelling challenge while having an order of magnitude fewer parameters than commonly used FCNs. © 2020 Copernicus GmbH. All rights reserved.