Lipid-extracted microalgae (LEM, KCTC 12236BP), a solid waste by-product obtained from algal biodiesel production, is typically considered a rich source of antioxidant compounds, including phenolic compounds. The purpose of this study was to apply a statistically-based methodology to enhance the extraction of total phenolic compounds (TPCs) and antioxidant activity (AA) from LEM and to verify the production of epigallocatechin gallate (EGCG), a bioactive material, under optimum conditions. The optimal extractions of TPC and AA were explored by varying the key variables, including the extraction temperature, ethanol concentration, extraction time, and ultrasonic power, through statistical optimization. The optimal extraction conditions were identified through 27 runs following the central composite design. The regression analyses of TPC and AA showed good fit of the experimental data to the second-order polynomial models, with coefficient of determination (R) values of 0.8769 and 0.8432, respectively. In the variation experiment, the maximum TPC and AA values of 9.8 mg GAE/g and 91.8% were obtained respectively with an extraction temperature of 74.4 °C, ethanol concentration of 55.4%, extraction time of 59.6 min, and ultrasonic power of 700 W. HPLC coupled with diode array detection was used to identify and quantify the phenolic compounds in the extracts, and EGCG (0.12 mg/g DM) was identified as a major peak in the analysis, demonstrating that high value-added material with a bioactive property can be produced from LEM. The results indicated that statistical optimization is applicable for optimizing the extraction of TPC and AA from LEM and provided a scientific basis for applying ultrasound-assisted extraction on an industrial scale by optimizing the conditions. LEM has a high TPC value, particularly with regard to EGCG, and excellent AA, considering it is highly used as a functional material for food, cosmetics, and medicine.