Network traffic analysis is crucial for understanding network behavior and identifying underlying applications, protocols, and service groups. The increasing complexity of network environments, driven by the evolution of the Internet, poses significant challenges to traditional analytical approaches. Graph Neural Networks (GNNs) have recently garnered considerable attention in network traffic analysis due to their ability to model complex relationships within network flows and between communicating entities. This scoping review systematically surveys major academic databases, employing predefined eligibility criteria to identify and synthesize key research in the field, following the Preferred Reporting Items for Systematic reviews and Meta-Analyses extension for Scoping Reviews (PRISMA-ScR) methodology. We present a comprehensive overview of a generalized architecture for GNN-based traffic analysis and categorize recent methods into three primary types: node prediction, edge prediction, and graph prediction. We discuss challenges in network traffic analysis, summarize solutions from various methods, and provide practical recommendations for model selection. This review also compiles publicly available datasets and open-source code, serving as valuable resources for further research. Finally, we outline future research directions to advance this field. This work offers an updated understanding of GNN applications in network traffic analysis and provides practical guidance for researchers and practitioners.