Fruit ripening is a complex process that involves the coordination of genes, hormones, and environmental factors. Understanding the mechanism of fruit ripening is important to improve shelf life and storage duration. Our current understanding of the fruit ripening mechanism is limited to model organisms such as tomatoes for climacteric fruits and grapes for non-climacteric fruits. Studies on the fruit ripening mechanism for other non-model fruits such as mangosteen, orange, and papaya are still limited. Recently, high-throughput sequencing and mass spectrometry technologies have generated abundant omics-based data from various fruits. While it is important to perform differential expression analysis to identify molecular changes, network analysis gives an added value by integrating all the omics data to infer the interactions between molecules. This provides a more comprehensive understanding of gene function, regulation, and mechanism to improve fruit shelf life. This review illustrates different types of network analysis and their applications in the identification of hub genes, proposing regulatory network models, metabolic shift detection, and guilt-by-association prediction of unannotated gene functions. The fruit ripening mechanism is also reviewed by integrating results from network analysis to fill in the gaps of knowledge. Lastly, the perspectives of network analysis in fruit ripening are discussed.