The disclosure describes an engine system having liquid and gaseous fuel systems, each of which injects fuel directly into an engine cylinder. A controller controls pumping of a liquefied natural gas (LNG) in the gaseous fuel system. In a pump cycle, a pumping piston is moved in an intake direction over an intake stroke such that the pumping piston produces a negative pressure that draws LNG from a tank fluidly connected to the pumping element into a pumping chamber of a body of the pumping element. The pumping piston is moved in an opposing power direction over a power stroke such that the pumping piston pumps compressed LNG out of the pumping chamber away from the tank. The pumping piston is moved over the intake stroke with an average intake velocity and over the power stroke with an average power velocity, which is greater than the average intake velocity.