A fuel injection apparatus for engines comprising a plurality of high pressure fuel pumps in each of which fuel supplied to a plunger room is compressed by a plunger driven by a fuel cam to reciprocate in a plunger barrel, the compressed fuel being discharged to a common rail at timing controlled by an electromagnetic valve, high pressure fuel accumulated in the common rail being injected into cylinders of an engine through injection valves at controlled timing, characterized in that a controller is provided which allows some of the plurality of high pressure fuel pumps to be made inoperative in discharging fuel to the common rail by controlling the electromagnetic valves of said some of the high pressure fuel pumps when the engine is operated with small/medium fuel injection quantity of smaller than a certain quantity, in that, when said some of the high pressure fuel pumps are made inoperative, the controller is configured to utilize the plunger stroke of each of the operative high pressure fuel pumps from near zero lift until a maximum lift so as to discharge a quantity of fuel including a quantity of fuel that was discharged from said some of the high pressure fuel pumps made inoperative by increasing discharge quantity of said each of the operative high pressure fuel pumps, and in that the controller comprises: a determining section of the number of plungers-to-be-used, configured to determine the number of high pressure fuel pumps, that is, the number of plungers-to-be-used needed to allow injection of a quantity of fuel corresponding with a detected engine load; a setting section of the order of plungers-to-be-used, configured to set the order to the high pressure fuel pumps among the plurality of the high pressure fuel pumps to be made operative in a range of low and medium load operation of the engine by controlling such that each of the high pressure pumps is made inoperative in determined order when common rail pressure detected by a pressure detector is low/medium so as to prevent uneven operation of a specific high pressure fuel pump; and a determining section of plungers-to-be-used configured to: determine the order of the high pressure fuel pumps to be operated upon receiving the number of plungers determined by the determining section of the number of plungers-to-be-used by calculation in the setting section of the order of plumgers-to-be-used; and set the high pressure fuel pumps operative. a determining section of the number of plungers-to-be-used, configured to determine the number of high pressure fuel pumps, that is, the number of plungers-to-be-used needed to allow injection of a quantity of fuel corresponding with a detected engine load; a setting section of the order of plungers-to-be-used, configured to set the order to the high pressure fuel pumps among the plurality of the high pressure fuel pumps to be made operative in a range of low and medium load operation of the engine by controlling such that each of the high pressure pumps is made inoperative in determined order when common rail pressure detected by a pressure detector is low/medium so as to prevent uneven operation of a specific high pressure fuel pump; and a determining section of plungers-to-be-used configured to: determine the order of the high pressure fuel pumps to be operated upon receiving the number of plungers determined by the determining section of the number of plungers-to-be-used by calculation in the setting section of the order of plumgers-to-be-used; and set the high pressure fuel pumps operative. determine the order of the high pressure fuel pumps to be operated upon receiving the number of plungers determined by the determining section of the number of plungers-to-be-used by calculation in the setting section of the order of plumgers-to-be-used; and set the high pressure fuel pumps operative.