Background: EUS-guided rendezvous procedure (EUS-RV) can be done by the transhepatic (TH) or the extrahepatic (EH) route. There is no data on the preferred access route when both routes are available. Study aim: To compare the success, complications, and duration of hospitalization for patients undergoing EUS-RV by the TH or the EH route. Patients and methods: Patients with distal common bile duct (CBD) obstruction, who failed selective cannulation, underwent EUS-RV by the TH route through the stomach or the EH route through the duodenum. Results: A total of 35 patients were analysed (17 TH, 18 EH). The mean procedure time was significantly longer for the TH group (34.4 vs. 25.7 min; p = 0.0004). There was no difference in the technical success (94.1 vs. 100%). However, the TH group had a higher incidence of post-procedure pain (44.1 vs. 5.5%; p = 0.017), bile leak (11.7 vs. 0; p = 0.228), and air under diaphragm (11.7 vs. 0; p = 0.228). All bile leaks were small and managed conservatively. Duration of hospitalization was significantly higher for the TH group (2.52 vs. 0.17 days; p = 0.015). Conclusions: EUS-RV has similar success rate by the TH or the EH route. However, the TH route has higher post-procedure pain, longer procedure time, and longer duration of hospitalization. The EH route should be preferred for EUS-RV in patients with distal CBD obstruction when both access routes are technically feasible.