To investigate the relationship between simultaneous prism and cover test (SPCT) and alternate prism and cover test (APCT) outcomes after exotropia surgery, and to identify characteristics associated with significant disparity between them. Review of sensorimotor outcomes 2 to 6 months after exotropia surgery identified patients with alignment documented by both SPCT and APCT at the same examination. Two hundred seventy-four and 319 patients had both measurements recorded at distance and near, respectively. Correlation between the SPCT and APCT and range of APCT when the SPCT measurement was zero were determined. Patient characteristics studied for association with a difference between the SPCT and APCT exceeding known APCT test-retest variability included age, visual acuity, fusion, intermittency, pattern, preoperative and postoperative angle, and treatment with or without medial rectus resection. SPCT and APCT outcomes were strongly correlated (P < .001), significantly different (P < .001), and linearly related. The percentage of patients who were orthotropic (SPCT = 0) was 76% at distance and 80% at near. Misalignment of 10 prism diopters (PD) or less by the APCT was present in 92% of orthotropic patients at distance and 84% at near. Surgery without medial rectus resection (P = .015), larger preoperative angle (P = .003), intermittent exotropia (P = .028), and postoperative exotropia rather than esotropia (P < .001) were associated with a significant SPCT-APCT difference. Although a greater postoperative SPCT-APCT disparity was confirmed for patients with intermittent exotropia, it also independently associated with a larger preoperative deviation and surgery without medial rectus resection. Performing medial rectus resection, a surgeon's prerogative, provides more apparently consistent postoperative alignment characterized by less SPCT-APCT disparity. [J Pediatr Ophthalmol Strabismus. 2017;54(4):222-230.].