Importance This is the first comprehensive comparison between ab interno approach and ab externo approach for microcatheter-assisted trabeculotomy in primary congenital glaucoma with clear cornea. Background Ab externo microcatheter-assisted trabeculotomy is considered to be the gold standard for primary congenital glaucoma. The novel ab interno approach would intuitively be similar to ab externo approach for microcatheter-assisted trabeculotomy in eyes with clear cornea; however, there is no evidence yet. Design Non-contemporary comparison of retrospective case series. Participants Fifty-eight and fifty-seven consecutive primary congenital glaucoma eyes with clear corneas underwent ab interno and ab externo microcatheter-assisted trabeculotomy, respectively. Methods Retrospective comparison of clinical outcomes. Main Outcome Measures Surgical success was defined as a postoperative intraocular pressure of <= 21 mmHg with at least a 30% reduction from preoperative IOP with or without the use of anti-glaucoma medication (qualified and complete success, respectively). Results The qualified success rate (87.9% vs 82.2%, P = .40) and complete success rates (81.0% vs 73.3%, P = .32) were comparable between groups. Complications were minimal and comparable. Less than 360 degrees trabeculotomy (P = .009) and a higher number of previous surgeries (P = .03) were both associated with worse surgical outcomes. Conclusions and Relevance Ab interno approach provide good and comparable outcomes as ab externo approach for microcatheter-assisted trabeculotomy in primary congenital glaucoma eyes with clear cornea. It should be considered as the initial choice in these patients with the benefit of sparing conjunctiva. Successful trabeculotomy with either technique during the first attempt is critical to overall success and underscores the need for proficiency before independent practice.