The difference in intraocular pressure (IOP) dynamics between trabeculectomy and topical instillation of timolol was compared in a rabbit ocular hypertension model. Twenty New Zealand white rabbits trabeculectomized with subconjunctival retention of 0.3 mL C3F8 gas in the right eyes were used as animal models. One week and three weeks after the operation, the left eyes of the rabbits were given three drops of 0.5% timolol, and IOP dynamics were compared between the two fellow eyes after intravenous infusion of 0.9% NaCl sterile solution. There were four parameters available in comparing IOP dynamics: Time Needed to Reach Peak IOP (TNRPI); Ascending Slope (AS); Peak IOP (PI); and Time Needed to Return to the Original IOP (TNROI). By this method, it was noted that, at the 7th day after the operation, the eyes trabeculectomized with subconjunctival retention of C3F8 gas had lower IOPs than the eyes that received topical instillation of timolol (baseline IOP: 14.7 +/- 4.2 vs. 19.5 +/- 2.5, p < 0.001, PI: 16.4 +/- 5.2 vs. 26.2 +/- 9.3, p < 0.001). In addition, at the 21st postoperative day, after intravenous infusion of 0.9% NaCl solution, the operated eyes showed less IOP spiking than the eyes that received topical instillation of timolol (TNRPI: 5.7 +/- 2.1 vs. 3.9 +/- 2.3, p = 0.014; AS: 0.8 +/- 0.5 vs. 2.7 +/- 2.6, p = 0.003; PI: 21.2 +/- 7.8 vs. 27.9 +/- 8.6, p = 0.014; and TNROI: 8.4 +/- 6.5 vs. 12.6 +/- 7.3, p = 0.06). These results suggested that trabeculectomy, rather than topical timolol, yielded better protection against IOP spiking in a transient rabbit ocular hypertension model.