In this paper, we present GRAPHIA, a novel approach for generating accurate call graphs of JavaScript programs. Existing static analysis techniques have limitations in generating incomplete or inaccurate call graphs due to the complex language features of JavaScript. GRAPHIA predicts missing call edges by predicting link pairs based on graph neural networks (GNNs) using inaccurate static call information and dynamic execution information. We construct program graphs containing various types of edges and conduct experiments on 50 popular JavaScript libraries. As a result, we show that the correct target function is a top candidate in more than 42% of outstanding call cases and is ranked within the top five candidates in more than 72% of cases, thereby enhancing the efficiency of static analysis. This is the first attempt to apply GNN-based link prediction to the entire program graph.