BackgroundPlant-parasitic nematodes (PPNs) that cause most damage include root-knot nematodes (RKNs) which are a major impediment to crop production. Root-knot nematodes, like other parasites, secrete proteins which are required for parasite proliferation and survival within the host during the infection process.ResultsHere, we used various computational tools to predict and identify classically and non-classically secreted proteins encoded in theMeloidogyne javanicagenome. Furthermore, functional annotation analysis was performed using various integrated bioinformatic tools to determine the biological significance of the predicted secretome. In total, 7,458 proteins were identified as secreted ones. A large percentage of this secretome is comprised of small proteins of ≤ 300 aa sequence length. Functional analyses showed thatM. javanicasecretome comprises cell wall degrading enzymes for facilitating nematode invasion, and migration by disintegrating the complex plant cell wall components. In addition, peptidases and peptidase inhibitors are an important category ofM. javanicasecretome involved in compatible host-nematode interactions.ConclusionThis study identifies the putative secretome encoded in theM. javanicagenome. Future experimental validation analyses can greatly benefit from this global analysis ofM. javanicasecretome. Equally, our analyses will advance knowledge of the interaction between plants and nematodes.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12864-023-09366-6.