Mesenchymal stem cells (MSCs) have significant anti-inflammatory properties and are beneficial in rodent models of pancreatitis. The safety and efficacy of MSCs is unknown in dogs with acute pancreatitis (AP). Dogs with AP who were treated with MSCs (n = 4) were identified prospectively for this pilot study from an academic hospital. Serum Spec cPL and C-reactive protein (CRP) concentrations were measured on the day of MSC administration and 2 days later. The clinical severity, via the Modified Clinical Activity Index (MCAI), was also calculated. Two dogs received MSCs shortly after AP diagnosis, while the remaining dogs received MSCs due to clinically refractory disease. Changes in Spec cPL, CRP, and MCAI in the MSC-treated dogs were compared to a control population (n = 7) receiving the standard-of-care treatment for AP. No significant differences were noted between the populations for changes in Spec cPL (p = 0.79), CRP (p = 0.67), or MCAI (p = 0.91). However, subjective clinical improvements were noted within 24 h of MSC infusion in the two dogs with previously refractory disease. MSC infusions appear safe in the management of AP in dogs and may be considered in refractory disease. However, given the nature of this pilot study and its limitations, larger randomized controlled clinical trials are needed to truly evaluate the efficacy of MSC infusions in dogs with AP.