IntroductionTrabeculotomy and combined trabeculotomy–trabeculectomy (CTT) are major surgical options for primary congenital glaucoma (PCG). However, it is unclear which of these two surgical procedures should be recommended as the optimum first-line treatment for PCG. This trial aims to determine whether the outcomes of trabeculotomy are non-inferior to those of CTT in moderate PCG with a horizontal corneal diameter (HCD) of 12–14 mm.Methods and analysisThis is a 3-year, non-inferiority, prospective, randomised controlled trial. We plan to recruite 248 participants (aged ≤3 years) with PCG with an HCD of 12–14 mm from the Department of Glaucoma, Zhongshan Ophthalmic Center, Guangzhou, China. One eye per participant will be randomly (1:1) assigned to receive trabeculotomy or CTT. The primary outcome is the 3-year postoperative success rate in lowering intraocular pressure (IOP), and the secondary clinical outcomes will include IOP reduction, visual acuity, HCD, central corneal thickness, axial length, cup–disc ratio, refractive error and postoperative complications. Data will be analysed by the intention-to-treat principle.Ethical approval and disseminationThe study protocol has been approved by the ethics committee of Zhongshan Ophthalmic Center (2014MEKY023) and the ‘5010 Plan’ evaluation committee at Sun Yat-Sen University, Guangzhou, China. The results will be disseminated in international academic meetings and published in peer-reviewed journals.Trial registration numberChinese Clinical Trial Registry, ChiCTR-IOR-14005588; Date registered: 20 November 2014.