Open-source development has revolutionized the software industry by promoting collaboration, transparency, and community-driven innovation. Today, a vast amount of various kinds of open-source software, which form networks of repositories, is often hosted on GitHub – a popular software development platform. To enhance the discoverability of the repository networks, i.e., groups of similar repositories, GitHub introduced repository topics in 2017 that enable users to more easily explore relevant projects by type, technology, and more. It is thus crucial to accurately assign topics for each GitHub repository. Current methods for automatic topic recommendation rely heavily on TF-IDF for encoding textual data, presenting challenges in understanding semantic nuances. This paper addresses the limitations of existing techniques by proposing Legion, a novel approach that leverages Pre-trained Language Models (PTMs) for recommending topics for GitHub repositories. The key novelty of Legion is three-fold. First, Legion leverages the extensive capabilities of PTMs in language understanding to capture contextual information and semantic meaning in GitHub repositories. Second, Legion overcomes the challenge of long-tailed distribution, which results in a bias toward popular topics in PTMs, by proposing a Distribution-Balanced Loss (DB Loss) to better train the PTMs. Third, Legion employs a low-confidence filter to eliminate vague recommendations, thereby improving the precision of PTMs. Our empirical evaluation on a benchmark dataset of real-world GitHub repositories shows that Legion can improve vanilla PTMs by up to 26% on recommending GitHub topics. Legion also can suggest GitHub topics more precisely and effectively than the state-of-the-art baseline with an average improvement of 20% and 5% in terms of Precision and F1-score, respectively.