The rotational behavior of the web-flange junctions (WFJs) of a pultruded GFRP bridge deck system was investigated. The rotational response of three WFJ types was characterized. An experimental procedure based on three-point bending and cantilever experiments conducted on the web elements and simple analytical models was used. The WFJs generally exhibited non-rigid and nonlinear behavior. The overall moment-rotation relationships, rotational stiffness, strength and failure modes differed depending on the web type, the location of the WFJ within the deck profile, the initial imperfections and the direction of the bending moment applied. Simplified expressions to model the WFJ rotational behavior were derived. The validity of the experimental and idealized rotational responses was assessed by means of numerical simulations of full-scale experiments conducted on the GFRP deck.