A hypertensive phase frequently develops in the early postoperative period after glaucoma shunt operations. Anti-glaucoma eye drop use is essential when postoperative intraocular pressure (IOP) is not controlled. We investigated whether the use of early topical anti-glaucoma medication affects wound healing following glaucoma tube surgery. Eyes were randomly assigned to receive topical aqueous suppressant (timolol-dorzolamide fixed combination), prostaglandin (PG) analogue (travoprost), or normal saline (control group). First, we observed the effects of topical eye drops on Tenon's tissue in non-operated eyes in rabbits. Second, we examined the effects of these eye drops on rabbit eyes that underwent Ahmed glaucoma drainage device implantation, including the effects on the histopathological appearance of their blebs. Interleukin-2 in the Tenon's tissue was elevated in the PG group when compared to the control and aqueous suppressant groups (P = 0.006). In non-operated eyes, IOP was similar among the groups (P = 0.545). After glaucoma implant surgery, the average height of the inner collagenous layer and the average height of the α-SMA-positive blebs were the least in the aqueous suppressant group (P = 0.013, P = 0.001, respectively) at 4 weeks postoperatively. IOP was lower in the aqueous suppressant group than that in the control and PG groups (P = 0.001) following tube surgery. After Ahmed tube surgery, early treatment with aqueous suppressant decreased fibrosis in the bleb, but early treatment with the PG analogues did not.