Long-range surface plasmon Y-junctions are demonstrated as sensors for the detection of bulk refractive index changes in solution and for protein binding. Using a fully-cladded Au stripe waveguide as a reference channel, common drift and noise in the system can be eliminated, relaxing the need for precise optical alignments. The performance of the structure is discussed theoretically, then bulk sensing is carried out experimentally with five solutions of different refractive indices, and protein sensing is demonstrated through physisorption of bovine serum albumin on a carboxyl-terminated Au stripe. The Y-junction biosensor demonstrated a very good ability to perform drift and noise suppression for fast and accurate biosensing.