Systems and methods for inter-arm registration include a computer-assisted system having a control unit coupled to a repositionable arm of a computer-assisted device. The control unit is configured to: receive, from an imaging device, successive images of an instrument mounted to the repositionable arm; determine an observed velocity of a feature of the instrument; determine an expected velocity of the feature of the instrument based on kinematics of the repositionable arm; transform the observed velocity and/or the expected velocity to a common coordinate system using a registration transform; determine an error between directions of the observed and expected velocities in the common coordinate system; and update the registration transform based on the determined error. In some embodiments, the instrument is a medical instrument and the imaging device is an endoscope. In some embodiments, the control unit is further configured to control the instrument using the registration transform.