Mitogen-activated protein kinase (MPK) cascades are universal signal transduction modules regulating vegetative and reproductive development of plants. However, the molecular mechanisms of SlMPK4 gene in tomato pollen and fruit development remain elusive. SlMPK4 is preferentially and highly expressed in tomato stamens and its mRNA levels increase during early flower development, peaking at the mature pollen stage. Either up- or down-regulation of SlMPK4 expression had no significant effect on tomato vegetative growth. Though, RNAi-mediated suppression of SlMPK4 caused defects in pollen development, resulting in pollen abortion. The aborted pollen grains were either malformed or collapsed and completely lacked viability, resulting in predominately reduced fruit set rate in RNAi lines compared with control and overexpressed transgenic plants. Interestingly, the seed development was inhibited in RNAi-lines. Moreover, >12% of emasculated RNAi flowers developed seedless fruits without pollination. Anthers can produce typical microspore mother cells (MMCs) as well as uninucleate microspores, according to cytological investigations, while binucleate pollen ceased to produce typical mature pollen. The pollen abortion was further confirmed by transmission electron microscopy (TEM) analysis at binucleate stage in RNAi plants. The exine layer in aberrant pollen had a normal structure, while the intine layer appeared thicker. Suppression of SlMPK4 affects the transcript level of cell wall formation and modification, cell signal transduction, and metabolic and biosynthetic processes related genes. A subset of genes which may be putative substrates of plant MAPKs were also differentially changed in RNAi transgenic flowers. Taken together, these results suggest that SlMPK4 plays a critical role in regulating pollen development and fruit development in tomato plants.