The present study was intended to enhance the permeation of artemether and lumefantrine by encapsulating in dissolvable microneedle arrays for extended action. Lumefantrine-nanoparticles were synthesized using chitosan mediated gelation and optimized by 22 factorial designs. The particle size, zeta potential and % entrapment efficiency of the optimized nanoparticles F5 were 105 ± 3.64 nm, 24.4 ± 0.54 mV and 83.94 ± 1.71%, respectively. The nanoparticles showed a controlled-release of 79.15 ± 2.45% for lumefantrine after 24 h and stability for 6 months. A combination of biocompatible polymers (PVA and PVP K - 12) was used to develop dissolvable microneedle of artemether co-loaded lumefantrine nanoparticles. The SEM and TEM analysis confirmed the needle-shaped morphology with a size of 672 ± 0.99 μm. The in-vitro release of microneedle showed biphasic release pattern for both artemether and lumefantrine, with an initial burst followed by controlled-release profile. The ex-vivo study of optimized formulation showed 70.94 ± 2.45% and 65.87 ± 1.94% permeation for artemether and lumefantrine, respectively, after 24 h. Thus, microneedle-based delivery provides an alternative to painful intravenous administration and a promising approach to increase the penetration of drugs across the skin barrier. Graphical abstract Fabrication of microneedle arrays of artemether co-loaded with lumefantrine nanoparticles.