This study cloned, expressed, purified, and characterized the bacteriophage-derived endolysin LysCPQ7 from Clostridium perfringens phage CPQ7 and evaluated its potential as a natural biocontrol agent in milk and cheese. LysCPQ7 exhibited remarkable thermal and pH stability, retaining strong lytic activity after exposure to temperatures up to 60°C and showing optimal activity under alkaline conditions (pH 9–11). The enzyme efficiently lysed all tested C. perfringens strains while showing no activity against non-target bacteria. In broth culture, LysCPQ7 reduced viable bacterial counts by 3.86 log CFU/mL after 6 hours. Furthermore, it significantly decreased C. perfringens populations in artificially contaminated milk and sliced cheese stored at 8°C and 24°C. These findings demonstrate that LysCPQ7 is a promising, environmentally stable endolysin with strong potential as a non-antibiotic biocontrol agent for improving the microbiological safety of dairy and fermented food products.