Applications of nanoparticle based fungicides have been increasing gradually in recent years because of many advantages over conventional chemical fungicides. This study presents fungicidal efficiency of sulfur nanoparticles (SNPs) against two phytopathogens, Fusarium solani (isolated from an infected tomato leaf, responsible for early blight and Fusarium wilt diseases) and Venturia inaequalis (responsible for the apple scab disease). Different parameters, such as particle size, particle concentration, surfactant media etc., which affect the efficiency of the fungicidal effect were also studied. It has been found that small sized particles (∼35 nm) are very effective in preventing the fungal growth. Microscopic study confirmed that the fungicidal effect is mainly because of the deposition of particles on the cell wall and subsequent damage of the cell wall. A plausible imbalance in the cell wall structure was also supported by a Biuret assay test. SNP based fungicide can be useful for the protection of important crops such as tomato, potato, apple, grape etc., from different diseases, mainly for “organic” farming.