Information on the spatial variability in plant disease is essential for location-based disease management. In the current study, the spatial distribution of tomato early blight disease was ascertained in District Gilgit, GilgitBaltistan, Pakistan. The comprehensive field survey was carried in two growing seasons (2014–2015), whereas in each growing season, 62 tomato fields were surveyed. Based on the distribution of disease, the respective thematic maps (incidence and severity) were prepared using Arc Map 10.1 with spatial analyst function of Arc GIS software by means of the inverse distance weight (IDW) interpolation method. Results indicate that early blight of tomato is spatially distributed in both growing seasons. However, in the first growing season, the disease incidence ranged from 10.22% to 44.16% and during later season 14.03–49.16%, whereas 5.37–16.40% and 6.52–26.94% severity was recorded. Furthermore, this information indicates that higher disease infestation occurred in 2015 in relation to 2014. This information linked to metrological data (temperature, precipitation and relative humidity), seemingly favored the early blight development during the growing period. Seven botanical extracts were tested against pathogen Alternaria solani at different concentrations (4, 6 and 8%). Results revealed that all tested plant extracts showed antifungal activities. However, at 8% concentration of plant extract, Datura starmonium, Berberis orthobotry, Podophyllum emodi and Uretica dioica exhibited >60%, while Peganum harmala, Artemisia maritima and Capparis spinosa <60% antifungal properties. The information generated due to this study could help the tomato growers regarding disease management and selection of resistant cultivars, improving profitability and food security in the Gilgit region.