Brazil is one of the largest melon producers worldwide, with its northeast region contributing 96% of the national production. However, fruit quality has been affected by diseases, recently associated with different Fusarium species, which have caused significant losses. The chemical product Imazalil is the most used to control post-harvest diseases in melons in Brazil, however, it is in the process of being banned. Furthermore, the market is increasingly demanding about food and environmental safety, increasing the need to search for alternative methods. From this perspective, this study aimed to evaluate the effect of thermotherapy on the management of rot caused by Fusarium species in Galia melons. Six times of immersion of the fruits in hot water at 58 ºC (0, 30, 60, 90, 120, and 150 s) and one chemical treatment (Imazalil fungicide) were evaluated for each species of Fusarium evaluated (F. falciforme and F. sulawesiense). The severity of the disease in fruits subjected to heat treatment after 90 s did not differ from chemical treatment, indicating that thermotherapy treatment can be used as an alternative to Imazalil. Thermotherapy also maintained the firmness of the fruits and increased the activity of peroxidase and polyphenol oxidase enzymes, increasing the fruits shelf life and activating defense pathways. Therefore, thermotherapy, at the temperatures and times evaluated, is recommended in the management of melon rot caused by Fusarium species.