Purpose: Manual measurements of strabismus are subjective, time consuming, difficult to perform in babies, toddlers, and young children, and rely on the examiner's skill and experience. An automated system, based on eye tracking and dedicated full occlusion glasses, was developed to provide a fast, objective, and easy-to-use alternative to the manual measurements of strabismus. This study tested the efficacy of the system in determining the presence of strabismus in children, as well as its type and the amount of deviation, in addition to differentiating between phorias and tropias. Design: A prospective, masked, inter-rater reliability study. Methods: A prospective, masked, cross-sectional study included 69 children, 3-15 years of age. A cover-uncover test and a prism alternating cover test (PACT) for the primary gaze, at a distance of 50 cm, were performed by 2 independent, masked examiners and by the automated system. Results: A high correlation was found between the automated and the manual test results (R = 0.9 and P < 0.001 for the horizontal deviation, and R = 0.91 and P < 0.001 for the vertical deviations, with 100% correct identification of the type of deviation). The average automated test duration was 46 seconds. The Bland-Altman plot, used to compare the 2 measurement methods, showed a mean value of −2.9 prism diopters (PD) and a half-width of the 95% limit of agreement of ±11.4 PD. Conclusion: The automated system provides precise detection and measurements of ocular misalignment and differentiated between phorias and tropias. It can be used in participants from the ages of 3 years old and up.