Papaya (Carica papaya L.) is one of the most important tropical fruits cultivated in tropical climate countries, and its production is often threatened by abiotic and biotic stressors, which significantly affect the yield and quality of papaya. In recent years, papaya genomics resources have become available, which has promoted papaya research and breeding. However, no dedicated digital platform for papaya genomics resources has been developed for the research and breeding communities. Potential users such as papaya geneticists, breeders, and pathologists require genomics resources and easy-to-handle tools to support their decision-making in selecting suitable genes and molecular markers. To address this issue, we developed a papaya knowledge-based digital platform, PapayaNetBase. PapayaNetBase comprises three papaya genome data sets (Eksotika, Sekaki, and Sunset varieties), genomic variation, transcriptomes, and metabolites. PapayaNetBase web interface was developed using WordPress, while MySQL was used as a database management system (DBMS). The database functionalities include search query and filter functions that can be performed based on the SNP identifier (ID), gene ID, pathway, and variety name. The search results are displayed in table format. The output of the search results can be downloaded in text, comma-separated value (CSV), or Excel formats. Data in FASTA format (i.e., scaffold, transcript and protein sequences) can be retrieved via the ‘Downloads’ menu. We also developed a knowledge graph dashboard for papaya traits utilising the Neo4j platform (http://bit.ly/papayanetbaseV1) to facilitate the easy dissemination of these genomics resources. Using the PapayaNetBase knowledge graph, users can visualise papaya traits with integrated genomics information, such as gene description, a protein–protein interaction network, gene ontology, and pathway. To our knowledge, this is the first integrated platform on papaya genomics that offers resources in a knowledge graph. PapayaNetBase aims to accelerate functional genomics and molecular marker analyses by enabling geneticists and breeders to explore and utilise the molecular information on papaya for application in papaya research and breeding programmes.