This paper presents a new cost-effective hybrid GFRP-Concrete deck system that the GFRP panel serves as both tensile reinforcement and stay-in-place form. In order to understand the fatigue behavior of such hybrid deck, fatigue test on a full-scale specimen under sagging moment was conducted, and a series of static tests were also carried out after certain repeated loading cycles. The fatigue test results indicated that such hybrid deck has a good fatigue performance even after 3.1 million repeated loading cycles. A three-dimensional finite element model of the hybrid deck was established based on experimental work. The results from finite element analyses are in good agreement with those from the tests. In addition, flexural fatigue analysis considering the reduction in flexural stiffness and modulus under cyclic loading was carried out. The predicted flexural strength agreed well with the analytical strength from finite element simulation, and the calculated fatigue failure cycle was consistent with the result based on related S-N curve and finite element analyses. However, the flexural fatigue analytical results tended to be conservative compared to the tested results in safety side. The presented overall investigation may provide reference for the design and construction of such hybrid deck system.