Objective To examine the relationship between after‐hours (ie, nights and weekends) emergency general surgery and morbidity or mortality in dogs and cats during hospitalization. Design Cross‐sectional study from September 1, 2013 to May 31, 2017. Setting University teaching hospital. Animals Four hundred seventy‐four dogs and 66 cats that underwent emergency general surgery (gastrointestinal, hepatobiliary, urogenital, soft tissue traumatic injury, splenectomy/excision of bleeding abdominal tumor, surgical revision, and negative exploratory categories) with the emergency surgery service. All patients were required to have complete medical records. Interventions None. Measurements and main results Study animals were grouped as exposed or not exposed to after‐hours emergency surgery. They were further classified as either postoperatively dead or suffering morbidity (yes or no). Additional exposure factors (eg, age, sex, American Society of Anesthesiology [ASA] status) were investigated. Multivariable logistic regression was used to identify and quantify any associations with mortality or morbidity. In dogs, exposure to after‐hours emergency general surgery was not associated with mortality or morbidity. In dogs, both mortality and morbidity were associated with ASA status. In cats, mortality was not examined because the number of dead cats was small (n = 5). The odds of morbidity were 3.4 times lower (1/0.29) in cats having emergency surgery after hours, compared to cats admitted during regular hours (odds ratio [OR], 0.29; 95% Confidence Interval (CI), 0.09‐0.93; P = 0.03). No other investigated exposure factors were associated with morbidity in study cats. Conclusions After‐hours emergency surgery in dogs was not associated with increased risk of mortality and morbidity at the study facility. Feline patients having emergency surgery during regular hospital hours had a higher risk of morbidity; further investigation of modifiable risk factors is warranted.