Background: Adequate surgical care of patients and concurrent training of residents is achieved in elective procedures through careful case selection and adequate supervision. Whether this applies when trainees are involved in emergency operations remains equivocal. The aim of this study was therefore to compare the risk of post-operative complications following emergency procedures performed by senior operators compared with supervised trainees. Methods: This is a retrospective cohort study examining in-hospital deaths of patients across all surgical specialties who underwent emergency surgery in Australian public hospitals reported to the national surgical mortality audit between 2009 and 2015. Multivariable logistic regression was used to explore whether there was an association between the level of operator experience (senior operator vs trainee) and the occurrence of post-operative surgical complications following an emergency procedure. Results: Our population consisted of 6920 patients. There were notable differences between the trainees and senior operator groups; trainees more often operated on patients aged over 80 years, with cardiovascular and neurological risk factors. Senior operators more often operated on very young and obese patients with advanced malignancy and hepatic disease. Supervised trainees had a lower rate of post-operative complications compared with senior operators; 18% (n = 396) and 25% (n = 1210), respectively (p < 0.05). Operations performed by trainees were associated with an 18% decrease (95% CI 5–29%; p < 0.05) in odds of post-operative complications compared with senior operators, adjusting for potential confounders. Conclusions: Contrary to popular belief, our results suggest that supervised trainees safely perform emergency operations, provided that cases are judiciously selected.