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The study aims to elaborate novel self-assembled liquid crystalline nanoparticles (LCNPs) for management of hormonal disturbances following non-invasive progesterone transdermal delivery.Fabrication and optimization of progesteroneloaded LCNPs for transdermal delivery were assessed via a quality by design approach based on 23 full factorial design. The design includes the functional relationships between independent processing variables and dependent responses of particle size, polydispersity index, zeta potential, cumulative drug released after 24 h and ex-vivo transdermal steady flux. The developed nanocarrier was subjected to TEM (transmission electron microscope) for morphological elucidation and stability study within a period of three months at different storage temperatures.The cubic phase of LCNPs was successfully prepared using glyceryl monooleate (GMO) via the emulsification technique. Based on the factorial design, the independent operating variables significantly affected the five dependent responses. The cubosomes hydrodynamic diameters were in the nanometric range (101–386 nm) with narrow particle size distribution, high negative zeta potential ≥−30 mV and entrapment efficiency ≥94%. The LCNPs succeeded in sustaining progesterone release for almost 24 h, following a non-fickian transport of drug diffusion mechanism. Ex-vivo study revealed a significant enhancement up to 6 folds in the transdermal permeation of progesterone-loaded LCNPs compared to its aqueous suspension. The optimized LCNPs exhibited a high physical stability while retaining the cubic structure for at least three months.Quality by design approach successfully accomplished a predictable mathematical model permitting the development of novel LCNPs for transdermal delivery of progesterone with the benefit of reducing its oral route side effects.