The effect of ultrasonication (25 kHz for 10 min) on physical, thermal, and structural properties and storage stability of palm oil-based oleogels prepared using different concentrations of carnauba wax (CW) (5% or 10%) were investigated and compared with oleogels prepared with a homogenizer (2000 rpm for 10 min). Overall, this study found that applying an ultrasonication process with higher CW concentration (10%) effectively improved the properties and stability of palm oil-based oleogel (p < 0.05). Oleogels processed with ultrasonication had higher lightness (L*), higher yellowness (b*), and lower redness (a*) than those processed with homogenizer (p < 0.05), irrespective of CW concentrations. However, a higher CW concentration (10%) increased the textural properties of oleogels such as hardness, stickiness, and tackiness as compared to oleogels with a lower CW concentration (5%) (p < 0.05). Thermal properties including melting onset temperature, melting peak temperature, and melting enthalpy were found to be significantly higher in ultrasonication-processed oleogels with high CW concentration (p < 0.05). Furthermore, the microscopic examination of the oleogels exhibited a strong gel network when prepared using a high concentration of CW and processed with ultrasonication. Fourier Transform Infrared (FTIR) spectra of oleogels revealed that strong intra- and intermolecular interactions were formed by hydrogen bonding between CW and palm oil. X-ray diffraction (XRD) showed a smooth and fine structural network of oleogels and proved that ultrasonication increased the structural properties of oleogel. Moreover, oil loss and peroxide value of oleogels were increased during 90 days of storage (p < 0.05). However, oleogels processed with the ultrasonication had reduced oil loss and increased peroxidation stability during storage (p < 0.05). Overall, this study showed that application of ultrasonication with a higher CW concentration could improve properties and storage stability of palm oil-based oleogel.