The aim of current research work was to establish robust, sensitive, precise and selective reversed-phase high-performance liquid chromatography (RP-HPLC) method for the quantification of efinaconazole from microemulsion and microemulsion-gel based formulations for onychomycosis treatment. Chromatographic separation of efinaconazole was performed on Waters Inertsil® HPLC column, 5 µm (ODS-3V C₁₈, 250 × 4.6 mm). The mobile phase was optimized as mixture of X and Y components in 20:80 v/v proportion (X component contains 0.01M phosphate buffer having pH 5.5 and acetonitrile in 75:25 v/v proportion and Y component contains acetonitrile) and the flow rate optimized at 1 mL min⁻¹. Efinaconazole detection and quantification was done at a wavelength of 210 nm using a ultra-violet (UV) detector. Linear relationship was observed in method calibration curve for the concentration range of 50–150 µg/mL with r² value >0.99. Different stress conditions experiments were carried out for the efinaconazole method development such as in acidic, basic, oxidation, photo, thermal, and humidity condition and no unknown degradation products interference were found during the estimation of efinaconazole. Further, the matrix effect of a microemulsion based excipients like diethylene glycol monoethyl ether, caprylcaproyl macrogol glycerides, and glyceryl caprylate has been overcame by present method of analysis with no excipient's interference. The method for analysis of efinaconazole was accurate, precise with average recovery rate of 98.6–101.6% and percentage RSD for all parameters of chromatographic system were found to be not more than 2.0%. Further, the method can be rapidly and effectively applied for the quantification of efinaconazole drug content from a microemulsion and microemulsion based gel formulations. Abbreviations: AUC, area under a curve; RP-HPLC, Reversed-phase high-performance liquid chromatography; ICH, International Council for Harmonisation; LOD, limit of detection; LOQ, limit of quantification; UV, ultra-violet; RSD, relative standard deviation; N, number of theoretical plates; Smix, surfactant mixture.