The compatibility of elastomers used in engine fuel system with Fischer–Tropsch (FT) fuel is essential, but there is very limited research available on it. In this work, the compatibility between four types of commonly used elastomers in fuel system and FT fuel was experimentally investigated. The assessed elastomers including nitrile butadiene rubber (NBR), ethylene propylene diene-monomer rubber (EPDM), fluoroelastomer (FKM), and chlorinated polyethylene (CPE) were exposed to FT fuel which derived from natural gas for 21 days. The properties of the elastomers such as mass, volume, hardness, tensile strength, elongation at break, and tear strength were measured before and after immersion, at the same time the change rates of these properties were calculated. The results demonstrated that all properties of EPDM deteriorated significantly after soak, and its compatibility with FT fuel was the worst, making it unsuitable for FT engines. NBR, FKM, and CPE all showed low rates of property change, with FKM exhibiting the greatest compatibility performance with FT fuel. Additionally, the O-rings made of FKM were submerged in FT fuel and diesel for 7 days, 14 days, and 21 days, respectively. It was found that the mass and volume variations of FKM O-rings in FT fuel were negligible and comparable with those of diesel fuel.