ABSTRACT The accurate automated classification of variable stars into their respective subtypes is difficult. Machine learning–based solutions often fall foul of the imbalanced learning problem, which causes poor generalization performance in practice, especially on rare variable star subtypes. In previous work, we attempted to overcome such deficiencies via the development of a hierarchical machine learning classifier. This ‘algorithm-level’ approach to tackling imbalance yielded promising results on Catalina Real-Time Survey (CRTS) data, outperforming the binary and multiclass classification schemes previously applied in this area. In this work, we attempt to further improve hierarchical classification performance by applying ‘data-level’ approaches to directly augment the training data so that they better describe underrepresented classes. We apply and report results for three data augmentation methods in particular: Randomly Augmented Sampled Light curves from magnitude Error (RASLE), augmenting light curves with Gaussian Process modelling (GpFit) and the Synthetic Minority Oversampling Technique (SMOTE). When combining the ‘algorithm-level’ (i.e. the hierarchical scheme) together with the ‘data-level’ approach, we further improve variable star classification accuracy by 1–4 per cent. We found that a higher classification rate is obtained when using GpFit in the hierarchical model. Further improvement of the metric scores requires a better standard set of correctly identified variable stars, and perhaps enhanced features are needed.