Ondansetron is a serotonin receptor antagonist for treating nausea and vomiting. Its multiple daily doses and extensive first-pass metabolism faced parenteral and oral administration challenges. The transdermal route enhances its bioavailability as it bypasses the first-pass effect. Invasome vesicles improve the skin permeation of ondansetron via its unique components, lecithin, limonene, and ethanol, which are considered efficient permeation enhancers. The current study intends to develop a gel containing ondansetron as invasomes vesicles with appropriate texture and efficient skin penetration. Two gelling agents, hydroxypropyl methylcellulose K4M and carbopol 934P, were used at two concentrations (0.5 and 1%, w/w). Formulas were evaluated regarding pH, content uniformity, viscosity, spreadability, and ex vivo permeation. The selected formula (F3), which contained ondansetron (5%, w/w) and used carbopol 934P at (0.5%, w/w), was homogeneous, with proper viscosity (21,500 ± 390 mPa.s) at rest and enough spreadability (3.4 ± 0.45 cm). The ex vivo permeation showed permeation flux (Jss) was (280.4 ± 3.5 g/cm2.h) with a shorter lag time (0.5 ± 0.1 h). Characterization studies revealed nanosized vesicles (Dav. = 202.9 ± 0.5 nm) as spherical shapes dispersed within a gel matrix. In vivo, skin irritation and histopathology studies using male Wistar albino rats demonstrated that (F3) was biocompatible, with no irritation reported for six consecutive days. In conclusion, the invasomes gel of ondansetron utilizing carbopol (0.5%, w/w) was prepared for transdermal delivery, offering effective permeation and safe application. An invasomes-loaded gel is considered a novel formulation, giving an efficient and realistic therapeutic option for treating vomiting.