Fungal pathogens destruct the quality and quantity of tomato production and cause health hazards to the consumers as well as economic loss to the traders. This study was carried out to identify some fungal diseases associated with post-harvest deterioration of stored tomato fruits in three vegetable markets of Lagankhel, Balkhu and Kalimati of Kathmandu Valley. The samples were collected from selected sites in three separate trials and cultured in Potato Dextrose Agar. During investigation, 16 species belonging to 15 genera of fungi were identified. They were Alternaria alternata, A. solani, Aspergillus niger, Botrytis cinerea, Cladosporium fulvum, Colletotrichum truncatum, Curvularia tetramera, Fusarium oxysporum, Geotrichum candidum, Mucor mucedo, Penicillium notatum, Phytophthora infestans, Phoma exigua, Pullularia pullulans, Pythium aphanidermatum and Rhizopus stolonifer. These were responsible for 15 different diseases of Alternaria fruit rot, Anthracnose, Black mold rot, Botrytis Bunch Rot, Damping off/ fruit rot, Drechslera mold, Fusarium rot, Mucor rot, Penicillium rot, Phoma blight, Phytophthora rot, Rhizopus rot, Russet, Scab and Sour rot. The presence of these fungi and corresponding rot diseases on stored tomato indicate the need for management of fungi, farm sanitation and improved market in order to prevent field-to-storage transmission of pathogens.