Objective: To evaluate the efficacy of 5-fluorouracil (5-FU) needling of encapsulated blebs (EBs) after Ahmed glaucoma valve (AGV) implantation in patients with medically uncontrolled secondary glaucoma. Methods: Thirty-eight eyes of 37 patients who underwent AGV implantation due to secondary glaucoma with EB were recruited in this retrospective non-randomized study. 5-FU needling (0.1 mL of 50 mg/mL) was performed for the restore of the aqueous outflow. Success after needling was defined as last intraocular pressure (IOP) <= 21 mmHg or >= 6 mmHg (with or without the use of antiglaucoma medication) without loss of light perception. Results: The mean follow-up time was 14.5 +/- 8.5 (5-36) months after needling. The mean interval between the AGV implantation and the needling was 10.2 +/- 7.5 (2-32) weeks. Patients were examined after needling at the 2nd hour, 1st week, 1st month, 3rd month, 6th month, and at the final visit. The success rates were 84.2%, 94.7%, 94.7%, 86.8%, 83.3%, and 71.1%, respectively. The Kaplan-Meier survival analysis revealed 96.4%, 77.4%, and 60.3% cumulative predictive success rates for the 6th, 12th, and 24th months, respectively. The mean IOP before needling was 28 +/- 8.4 mmHg. At the final visit, the mean IOP was 18.1 +/- 7.5 mmHg (p <= 0.001). Complications after needling included Seidel without hypotony (three eyes, 7.9%), hyphema (one eye, 2.6%), and decompression retinopathy (one eye, 2.6%). Neovascular glaucoma was the only factor that affected efficacy of treatment negatively (p = 0.003). Conclusions: Bleb needling with 5-FU seems to be a safe and effective method in patients with EB formation after AGV implantation in secondary glaucoma cases.