To evaluate the effect of creating a full-thickness prophylactic scleral window (PSW) during Ahmed glaucoma valve (AGV) surgery on the rate of postoperative choroidal effusion and choroidal drainage surgery. In this retrospective matched case-control study, after insertion of AGV tube a PSW was created in one group. The control-matched group had AGV without a PSW. Primary outcome measures were the rate of choroidal effusion formation and choroidal drainage surgery. In total, 544 patients (604 eyes) had undergone AGV implantation from 2013 to 2017. The PSW group consisted of 111 eyes of 111 patients and the control group had 111 eyes of 98 matched patients. There were no differences for systemic diseases, number of anti-glaucoma drugs, aspirin use, smoking, laterality of the operated eye, axial length, and central corneal thickness between the groups. Out of 12 eyes with choroidal effusion, only one belonged to the PSW group (P=0.02). Six eyes in the control group needed choroidal drainage surgery, but none of the eyes in the PSW group required this procedure (P=0.02). No intra- and postoperative issues were observed at the site of the scleral window in the PSW group. PSW creation during AGV surgery is a safe method to decrease the rate of choroidal effusion and choroidal drainage surgery.