There is provided a high pressure fuel pump control system for an internal combustion engine which enables fuel pressure control with high precision without being restricted by the number of cylinders of the internal combustion engine or the number of phase sensor signals and the number of cam noses which vertically drives a plunger of a high pressure fuel pump even when a camshaft phase varies by a variable valve timing mechanism by using the high pressure fuel pump with a solenoid valve. The control system has a means which changes an effective stroke by driving the solenoid valve in the high pressure fuel pump, and has a means which changes the drive timing of the high pressure fuel pump based on a cylinder recognition value of the internal combustion engine with the cam angle detecting means as an origin.