Background: Mycosporine-like amino acids (MAAs) are ultraviolet-absorbing metabolites found in cyanobacteria, fungi, algae, and animals, known for their antioxidant and anti-inflammatory properties. Objectives: This study aimed to optimize MAAs extraction from Fischerella sp. F5 using experimental design techniques. Methods: The central composite design was employed to determine the optimal levels of five factors: Total extraction time, temperature, sonication time, methanol ratio, and solvent volume. Each run involved extracting 100 mg of dried biomass under the specified conditions. Mycosporine-like amino acids content was quantified using high performance liquid chromatography (HPLC), and the antioxidant activity of the extract was assessed using the DPPH radical scavenging test. The best model was selected based on the highest R2 value, and the optimized extraction conditions were determined. Results: Mycosporine-like amino acids content in the final extracts ranged from 27.7% to 89%, with antioxidant activities ranging from 15% to 59.3%. Overall, all factors showed a positive correlation with MAAs content in the final extract. However, no significant model was established to correlate extraction conditions with MAAs purity ratio (MAA%) or extract antioxidant activity. Conclusions: The bioactivity of partially purified MAAs may be influenced by factors such as associated impurities extracted alongside MAAs, which were not investigated in this study. Further research is necessary to identify the exact factors affecting MAAs extraction yield and purity, aiming to obtain partially purified MAAs extracts with optimal bioactivity.