Hemodialysis (HD) catheter dysfunction compromises HD adequacy and increases the cost of patient care. Repeated administration of alteplase in HD catheters typically produces only short-term benefits. The purpose of this study was to design, implement, and evaluate the efficacy of an experimental alteplase algorithm to manage HD catheter dysfunction. This was a two-part prospective nonrandomized study. Baseline data of alteplase use and catheter exchange were collected during part 1 of the study. Part 2 consisted of the alteplase algorithm implementation and repeat collection of catheter data. Rates of alteplase use and catheter exchange per 1000 catheter-days were the primary and secondary outcomes of the study. One hundred and seventy-two catheters in 131 patients were followed prospectively during the course of the study. The adjusted relative rate (RR) of alteplase use showed no significant difference between both parts of the study, adjusted RR: 1.10, 95% confidence interval (CI) (0.73–1.65). Similarly, catheter exchange rates were not significantly different over the duration of the study (1.12 vs. 1.03 per 1000 catheter-days). However, waiting time for catheter exchange increased from 20.36 ± 14 days in part 1 to 38.42 ± 28 days in part 2 (P < 0.05). The alteplase algorithm did not significantly reduce alteplase use. This may be partially explained by repeated use of alteplase in part 2, due to longer waiting times for catheter exchange procedures.