The objective of the current study was to develop ziprasidone hydrochloride monohydrate (ZHM) nanocrystal-based orally dispersible tablet (ODT) formulations. Design of experiment approach was used to develop ODTs. The tablets were compressed using direct compression method and characterized with quality control tests. In vitro dissolution studies and Caco-2 cell permeability tests were executed. The hardness and friability values of nanocrystal-based ODTs were found 31.2 N and 1.05%, respectively. The disintegration time was below 10 s. Dissolution profile in pH 7.4 phosphate buffer showed that nanocrystal-based ODTs and commercial product were dissolved in 120 min 58.98% and 16%, respectively. In pH 7.4 phosphate buffer with SLS, sample groups dissolved above 85% at the end of the study. Permeability value and cumulative ZHM amount on the cells were improved with nanocrystals. In conclusion, the novel formulation of ZHM nanocrystal-based ODTs was successfully developed for alternative dosage form.