Traditional Chinese Veterinary Medicine (TCVM), which can include treatment with Chinese herbal medicine, is being used increasingly in Western medicine to treat a variety of diseases in dogs. With the increased interest in Chinese herbal medicines, evidence-based research to prove efficacy and safety of these traditional medicines is necessary. The objective of this research was to compare the effectiveness of the Chinese herbal medicine, Da Xiang Lian Wan (DXLW), to the Western pharmaceutical, metronidazole, in the treatment of stress colitis in sheltered/rescued dogs utilizing a randomized controlled study with a hypothesis that successful treatment with DXLW would not be less than metronidazole. Fifty-six dogs were randomly assigned to either metronidazole treatment group or DXLW treatment group. Each medication was administered orally twice daily at recommended clinical doses for a maximum of 10 doses. The results indicate that dogs in the metronidazole treatment group had an 89% response rate (normal stools) within the 10 dose protocol while the DXLW group had a 97% positive response rate (p < 0.05, non-inferiority test). This study demonstrates that DXLW is as effective as metronidazole in resolving stress colitis in sheltered dogs and can be an effective alternative treatment for patients that do not respond to metronidazole or cannot tolerate it.