The objective of this study was to compare the efficiency of ultrasound-assisted extraction (UAE) and microwave-assisted extraction (MAE) methods for extracting lipids from the green microalga Chlorococcum novae-angliae. This study specifically focused on the fatty acid profiles of the extracted lipids, using ethanol as the solvent and wet biomass as the starting material. Ultrasound-assisted extraction yielded a maximum of 0.026 ± 0.001 g lipid/g wet biomass at a biomass ratio of 1:25 for 2 min with a 1-second cycle at 180 W and 20 kHz, which was 21% higher than that of microwave-assisted extraction conducted at a ratio of 1:30 for 2 min at 300 W and 35 °C. Ultrasound-assisted extraction enhanced saturated fatty acids (SFAs), which were 1.5 times higher than to microwave-assisted extraction, while microwave-assisted extraction significantly increased polyunsaturated fatty acids (PUFAs) by 4.4 times. The findings suggest that ultrasound-assisted extraction is more suitable for applications requiring high SFA content, such as in the fuel industry, whereas microwave-assisted extraction is preferable for sectors focused on fatty acid quality, such as food and health. This comparative analysis contributes to the literature by highlighting the impact of extraction methods on fatty acid profiles and supports sustainable development goals (SDGs), particularly SDG 12, by promoting environmentally friendly extraction techniques.