Ionic liquids (ILs) show remarkable performance in enhancing the naphthenic acid extraction efficiency and decreasing the extraction time. However, the ultrasonic-assisted IL-based extraction of naphthenic acid is merely addressed previously. Therefore, this study investigated the impact of essential ultrasonic parameters, including amplitude and time, on naphthenic acid extraction using different ILs, and the system was optimized for maximum extraction. The IL 1,8-diazobicyclo[5.4.0]-undec-7-ene (DBU) with thiocyanate anions revealed the highest efficiency in extracting naphthenic acid from a model oil (dodecane) at optimized conditions, and the experimental liquid–liquid equilibrium data were obtained at atmospheric pressure for the mixture of dodecane, [DBU], thiocyanate, and naphthenic acid. In addition, the influence of the chain length of the cation (hexyl, octyl, or decyl) on the extraction efficiency was also evaluated by determining the distribution coefficients, and the conductor-like screening model for real solvents (COSMO-RS) study was carried out at infinite dilution. It was found that [DBU-Dec] [SCN] gives the best extraction efficiency and has a distribution coefficient of 9.2707 and a performance index of 49.48. Based on these values, ILs can be ordered as follows: [DBU-Dec] [SCN] > [DBU-Oct][SCN] > [DBU-Hex][SCN] in the decreasing order of performance index 49.48, 41.58, and 28.13. Moreover, non-random two liquid and Margules thermodynamic models were employed to investigate the interaction parameters between the components. Both models showed excellent agreement with the experimental results and could successfully be used for ultrasonic-assisted IL extraction of naphthenic acid.