Embodiments described herein relate to systems and methods of cylinder deactivation in compression-ignition engines. An engine described herein can include N cylinders, with N being an integer of at least 2, with each cylinder including an inner surface, a piston disposed and configured to move in each cylinder of the N cylinders, an intake port, an exhaust port, and a fuel injector. The piston and the inner surface define a combustion chamber. A method of operating the compression ignition engine includes injecting a fuel into each of the combustion chambers, combusting substantially all of the fuel in the compression ignition engine, monitoring engine load of the compression ignition engine, and deactivating a cylinder of the N cylinders upon a decrease in load to less than (N−1)/N×FL, wherein FL is a full load at a given engine speed.