Management costs are rarely taken into account in marine protected area (MPA) design. We estimate the management costs of two different protection scenarios within a large proposed MPA, the Coral Sea in Australia. We use three methods to estimate costs: an existing model of global MPA management costs; a new statistical model based on Australian MPA management costs; and expert estimates that extrapolate from the adjacent Great Barrier Reef Marine Park. Both the new statistical model and expert estimates were relevant to both protection scenarios and indicate that a single large no-take reserve is less expensive to manage than a multiple-use MPA of the same area with a 30% no-take component. Expenses associated with compliance drive the difference in management cost between scenarios. Estimating management costs of MPA scenarios adds an important, though still challenging, financial perspective to MPA design.