Gaseous fuel downstream of a heat exchanger can be too cold for fuel system components when the temperature of engine coolant employed as a working fluid in the heat exchanger is too low to elevate gaseous fuel temperature, and it is possible for the engine coolant to freeze. A method of operating a cryogenic pump for controlling discharge temperature of a heat exchanger that vaporizes a process fluid received from the cryogenic pump with heat from a working fluid, where the cryogenic pump includes a piston reciprocatable in a cylinder between a proximate cylinder head and a distal cylinder head, includes monitoring at least one of process fluid temperature and working fluid temperature; retracting the piston during an intake stroke from the proximate cylinder head to the distal cylinder head; and extending the piston in a plurality of incremental discharge strokes until the piston travels from the distal cylinder head back to the proximate cylinder head. At least one of the number of incremental discharge strokes, a length of incremental discharge strokes and a rest period between incremental discharge strokes is selected such that at least one of the process fluid temperature and working fluid temperature is maintained above a predetermined level.