This study aimed to evaluate the remineralization effect of GERM CLEAN, a novel antibacterial peptide, on early enamel caries. Thirty human enamel blocks from thirty teeth were randomly divided into three groups: double distilled water (DDW group), GERM CLEAN (GC group), and 1000 ppm fluoride (NaF group). Specimens were demineralized for 3 days (pH 4.6) followed by pH cycling twice daily for 14 days. For a pH cycle, specimens received corresponding treatments for 5 min, then were immersed in demineralizing solution for 1 h, received corresponding treatments again, and finally were immersed in remineralizing solution (pH 7.0) for approximately 11 h. Specimens were washed with DDW after each treatment. Microindentation tests, atomic force microscopy (AFM), and transverse micro-radiography (TMR) were conducted to analyze enamel blocks. GC demonstrated a lower percentage of surface microhardness recovery (SMHR%) (p < 0.0001), rougher surfaces (p < 0.0001), deeper lesion depth (p = 0.001), and more mineral loss (p = 0.001) than NaF, but showed higher SMHR% (p < 0.0001), smoother surfaces (p < 0.0001), shallower lesion depth (p = 0.049), and less mineral loss (p = 0.001) than DDW. As a result, GERM CLEAN has the potential to promote the remineralization of demineralized enamel.