The objective of the present study was to prepare and evaluate a microemulsion-based hydrogel with high malleability as a transdermal delivery carrier for levamisole (LMS). A pseudo-ternary phase diagram and D-optimal mixture design were utilized to screen and optimize the microemulsion, and the formulation comprised 7.5% Maisine^TM35-1, 33% S_mix and 59.5% water. The microemulsion was physically stable with an average size of 19.3 ± 0.1 nm and zeta potential of −3.84 ± 0.05 mV. Moreover, a highly malleable alginate-boronic acid (alginate-BA) gel was prepared and could come into close contact with highly curved skin. The optimized microemulsion was loaded into alginate-BA gel and subjected to ex vivo and in vivo investigation. The microemulsion-based gel had desirable characterization, good stability and negligible skin irritation. The results of ex vivo permeation study showed that LMS achieved a significantly higher cumulative amount from the LMS-loaded microemulsion-based gel than that from the LMS-gel. The pharmacokinetic study showed a twofold increase in relative bioavailability compared to the commercial liniment. These results provide insight into the capability of the developed malleable microemulsion-based gel to enhance the transdermal permeation and bioavailability of LMS.