Controlling intake pressure in a gaseous fuel internal combustion engine includes calculating a control term in an intake pressure control loop based on a pressure error, and adjusting a throttle valve and a second valve responsive to the control term in first and second control loop cycles. The second valve is within a return conduit returning compressed gases from a location downstream a compressor to a location upstream. A pressure of gaseous fuel and air within the intake conduit is changed via the adjustments so as to reduce the pressure error.