A method of programming a variable resistance element to be operated with stability and at a high speed is provided. The method programs a nonvolatile variable resistance element (10) including a variable resistance layer (3), which changes between a high resistance state and a low resistance state depending on a polarity of an applied electric pulse, and a lower electrode (2) and an upper electrode (4). The method includes: writing steps (S11) and (S15) to cause the variable resistance layer (3) to change from the low resistance state to the high resistance state by applying a write voltage pulse; and an erasing step (S13) to cause the variable resistance layer (3) to change from the high resistance state to the low resistance state. In the writing steps, a write voltage pulse is applied between the electrodes so as to satisfy |Vw1|>|Vw| where Vw1 represents a voltage value of the write voltage pulse in the first writing step (S11) after manufacturing the variable resistance element (10) and Vw represents a voltage value of the write voltage pulse in writing steps after the first writing step (S15) after manufacturing the variable resistance element (10).