Lemon myrtle (Backhousia citriodora) is native to Australia and is well-known for its lemon aroma and traditional uses in foods and as a medicine. The leaves are rich in phenolics, and gallic acid and hesperetin are the major phenolic compounds. Microwave-assisted extraction (MAE) is known as an effective extraction technique for phenolics from plant materials. This study aimed to investigate the individual and interaction effects of microwave on the isolation of gallic acid and hesperetin from lemon myrtle leaf and quantify the part in total phenolic compound. This study also optimized the MAE conditions. Extraction solvent was acetone (50%) in water and extraction time, microwave power and sample to solvent ratio were tested for their optimal conditions. The results showed that extraction time and microwave power had a positive significant effect on gallic acid, but not on hesperetin; whereas, the sample to solvent ratio had a negative significant impact on both gallic acid and hesperetin. The optimal MAE conditions were 6 min, 630 W, and 2 g/100 mL. Under these conditions, 43.32 mg gallic acid and 21.51 mg hesperetin could be obtained from a gram of dry sample. These account for approximately 42% and 21% of extracted total phenolic and flavonoid content, respectively. The optimized MAE conditions are recommended for recovery of gallic acid and hesperetin from lemon myrtle leaves for further applications.