The objective of this study was to compare the outcomes of inferior oblique anterior transposition (IOAT) versus inferior oblique myectomy (IOM) in patients with primary inferior oblique overaction (IOOA) or secondary IOOA to superior nerve palsy. A systematic review and meta-analysis were performed using the Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) Guidelines and an electronic search was conducted to identify studies comparing IOAT versus IOM for IOOA. Residual inferior oblique function, reduction in hypertropia and post-operative complications were identified as primary outcomes. Secondary outcomes included superior oblique function, head tilt improvement, effect on the contralateral eye, operation time and macular changes. The analysis was based on fixed or random-effects modelling. Eleven studies enrolling 729 patients were identified. Inferior oblique function was not significantly different between both interventions, namely the elimination of IOOA (Odds Ratio[OR] = 0.97, P = 0.97), reduction in IOOA (Mean Difference[MD] = −0.06, P = 0.68), post-operative inferior oblique under-action (OR = 1.06, P = 0.83) and residual overaction (OR = 0.71, P = 0.15). Similarly, no significant difference was noted between both groups in reducing hypertropia. Regarding post-operative complications, no significant difference was observed, including the incidence of anti-elevation syndrome (P = 0.10). No significant difference was noted regarding superior oblique function, improvement in head tilt, effect on the contralateral eye and macular changes, although surgical time was shorter in the IOM group. In conclusion, IOAT and IOM are both effective surgical procedures in the management of IOOA as they produced comparable outcomes in the improvement in hypertropia, post-operative inferior oblique function and incidence of complications.