Purpose: To evaluate the effect of low-dose atropine on myopia control in children with a history of surgery for intermittent exotropia (IXT). Methods: We retrospectively reviewed the medical records of children who used 0.05% atropine for ≥ 1 year to control myopia progression. This group included 45 patients with a history of IXT surgery and 57 patients with no such history. The annual changes in spherical equivalent and axial length were compared 6 months before, 6 months after, and 1 year after atropine instillation between the IXT surgery group and myopia controls. In this comparison, the dominant eye was paired with the right eye and the non-dominant eye with the left eye. We also analyzed the difference between IXT surgery cases corrected within versus not within 10 prism diopters (PD) at the start of low-dose atropine treatment. Results: A total of 102 patients had an average of -3.81 ± 1.53 diopters (D) and used low-dose atropine for an average of 16.8 months from a mean age of 8.2 years. On average, the IXT surgery group underwent muscle surgery for 28.1 PD of IXT at 7.8 years. A year after instillation, the myopia progression rate was -0.52 ± 0.89 D/year and 0.27 ± 0.40 mm/year in the IXT surgery group compared to -0.47 ± 0.83 D/year and 0.31 ± 0.24 mm/year in the myopia control group with no significant differences. However, after 6 months of instillation, the dominant eye in the IXT surgery group exhibited a significantly faster myopia progression rate than the right eye in the myopia control group (-0.84 ± 1.61 D/year vs. -0.56 ± 0.80 D/year, p = 0.04; 0.27 ± 0.33 mm/year vs. 0.22 ± 0.21 mm/year, p = 0.02). No difference was found in the myopia control effect between corrected and uncorrected cases in the IXT surgery group. Conclusions The effect of low-dose atropine on myopia control in children after IXT surgery was similar to that in myopia controls. However, it was less effective in the dominant eye during the early treatment period.