A case-control study was conducted to identify exposure factors associated with gastrointestinal (GI) side effects (i.e., vomiting, diarrhea, or anorexia) in dogs after treatment with Chinese herbal medicine. Investigated exposure factors included age, gender, breed, spay/neuter status, body weight, presenting complaint(s) at admission, herbal treatment(s) used and duration of treatment, as well as other medication(s) and diet(s) used during treatment. A total of 34 case dogs and 34 control dogs were enrolled in the study. Using logistic regression analysis, short duration of treatment (≤ 5 days) was associated with a diagnosis of GI side effects in study dogs (p < 0.001). Although the frequency of dogs affected with side effects after treatment with Chinese herbal medicine is very low, traditional Chinese veterinary practitioners and dog owners are advised to monitor dogs for GI side effects during the first five days after treatment with Chinese herbal medicine.