This retrospective study was designed to investigate the effectiveness of tissue plasminogen activator-tobramycin antibiotic lock solutions (TPA/tobra ABLs) for prophylaxis of catheter-related bacteremia (CRB) in high-risk children on long-term hemodialysis. During the first 6 months (Era 1), the high-risk group was defined. These patients received TPA/tobra ABL prophylaxis after every hemodialysis treatment for the next 6 months (Era 2). The prophylaxis regimen was applied once a week for the third 6-months period (Era 3). Primary endpoints were CRB and infection-free catheter survival. There were 16,412 catheter days, and 95 cases of CRB in 43 children. The incidence of CRB was 5.8/1,000 catheter days. Significant decrease in the incidence of CRB was observed when prophylactic TPA/tobra ABL was used in the high-risk group (P = 0.0201). There was a tendency for less CRB when prophylactic ABL was applied after every hemodialysis session compared with once a week (P = 0.0947). The catheters in the high-risk group had shorter survival times than those in the average-risk group in Era 1 (P < 0.0001). However, both the overall and infection-free survival of the catheters in the high-risk group significantly improved while the patients were receiving TPA/tobra ABL prophylaxis, becoming similar to the outcomes of the catheters in the average-risk group and exhibiting statistically non-significant differences (P = 0.5571 and P = 0.9711, respectively). In conclusion, the TPA/tobra ABLs may effectively reduce the rate of CRB, and this may prolong both the overall and infection-free survival times of the catheters in the high-risk group.