Pinnipeds are major consumers in marine ecosystems, and understanding their energy budgets is essential to determining their role in food webs, particularly where there is competition with fisheries. Food consumption and energy expenditure have been evaluated in pinnipeds using different methods, but the use of heart rate to estimate energy expenditure is potentially a very powerful tool suited to the life history of these animals. We tested a procedure for the subcutaneous implantation of heart rate data loggers to determine whether heart rate could be recorded for ≥1 year in free-ranging pinnipeds, as it has been in birds. We implanted 3 captive California sea lions (Zalophus californianus) and 3 captive northern elephant seals (Mirounga angustirostris) with heart rate data loggers and monitored their recovery and behavior in a controlled environment. In both species, the implantation site allowed for excellent detection of the electrocardiogram, and we observed heart rate signatures characteristic of behaviors such as resting and diving. Although all 3 sea lions recovered well from the implantation surgery, all 3 elephant seals showed a substantial inflammatory response for unknown reasons, and we removed the implanted data loggers. Subcutaneous implantation of data loggers is a powerful technique to study physiology, energetics, and behavior in California sea lions, but more work is required to realize the potential of this technique in northern elephant seals.