In this paper, we introduce the citation data of the Czech apex courts (Supreme Court, Supreme Administrative Court and Constitutional Court). This dataset was automatically extracted from the corpus of texts of Czech court decisions - CzCDC 1.0. We obtained the citation data by building the natural language processing pipeline for extraction of the court decision identifiers. The pipeline included the (i) document segmentation model and the (ii) reference recognition model. Furthermore, the dataset was manually processed to achieve high-quality citation data as a base for subsequent qualitative and quantitative analyses. The dataset is available to the general public at GitHub.