A method and apparatus for controlling a walking assistance apparatus are provided. The apparatus may include a detector configured to detect a first step of a user, based on measured right and left hip joint angle information, a reconstructor unit configured to reconstruct knee joint information matched to the right and left hip joint angle information based on knee joint trajectory information in response to the user's steps, and a torque generator configured to generate a first torque applied to a first leg corresponding to the first step. The torque generator may generate the first torque, based on a second torque applied to a second leg that is opposite to the first leg and that corresponds to a second step preceding the first step.