Aspects are generally directed to multi-sensor boresight alignment methods and systems for a multi-spectral reimaging optical system. In one example, a multi-sensor boresight alignment system includes a system interface to receive a first image frame from a first sensor and a second image frame from a second sensor, the first image frame having a contrast within a first spectral band and including a first image of a plate having a pattern of apertures, and the second image frame having a contrast within a second spectral band and including a second image of the plate. The system includes a field programmable gate array (FPGA) coupled to the system interface, the FPGA configured to spot track each image frame to identify a corresponding centroid of the pattern of apertures and correct an optical alignment between the first and second sensors based on a position of the corresponding centroids.