A propulsion control system for a marine vessel includes a memory and a controller coupled to the memory. The controller is configured or programmed to, while performing dynamic positioning control of the marine vessel or in a case in which the marine vessel has changed to a mode in which the marine vessel is kept at a certain location, perform deceleration control to reduce a bow direction speed of the marine vessel. Alternatively, the controller is configured or programmed to, in a case in which the marine vessel has changed to a mode in which the marine vessel moves along a predetermined route, when the marine vessel deviates from the predetermined route in a bow direction of the marine vessel, perform deceleration control to prevent the marine vessel from moving in the bow direction.