Background: To assess the clinical effectiveness of orthoptic therapy in the postoperative stabilisation and rehabilitation of binocular function in children with intermittent exotropia (IXT) after surgery. Methods: This was a prospective, parallel, randomised controlled trial. A total of 136 IXT patients (aged from 7 to 17 years) who had been successfully corrected at 1 month after surgery were enrolled in this study, and 117 patients (58 controls) completed the 12-month follow-up visit. The primary outcome was established as the proportion of patients with suboptimal surgical outcomes, which were defined as: (1) exodeviation ≥10 prism diopters (PD) at distance or near using the simultaneous prism and cover test (SPCT), or (2) constant esotropia ≥6 PD at distance or near using SPCT, or (3) loss of 2 or more octaves of stereopsis from baseline. The secondary outcomes were the exodeviation at distance and near using the prism and alternate cover test (PACT), stereopsis, fusional exotropia control and convergence amplitude. Results: The cumulative probability of suboptimal surgical outcome by 12 months was 20.5% (14/68) in the orthoptic therapy group and 42.6% (29/68) in the control group. There was a significant difference between these two groups (χ2 = 7.402, p = 0.007). Improvements in stereopsis, fusional exotropia control and fusional convergence amplitude were found in the orthoptic therapy group. A smaller exodrift was found in the orthoptic therapy group at near fixation (t = 2.26, p = 0.025). Conclusions: Early postoperative orthoptic therapy can effectively improve the surgical outcome as well as stereopsis and fusional amplitude.