Mud pumping induced by repeated train passages is one of the most serious distresses not only for ballasted tracks but also for ballastless tracks. In this study both field and laboratory tests were performed to find out the main influencing factors and to further develop a new remediation method. Field observations showed that mud pumping in ballastless track mostly occurred at both ends of concrete base (the expansion joints), triggered mainly by the whipping effect of track vibration due to repeated train passages. Based on the results from cyclic uniaxial test on polyurethane-aggregate specimen, showing an excellent resilience behavior and a high and stable quasi-static elastic modulus under the stress amplitude of 80 kPa for 3 million cycles, a remediation method with Polyurethane Chemical Injection (PCI) was developed for mud pumping in ballastless track, which consisted in injecting polyurethane chemical materials into roadbed at an angle of 45° to get a large stabilized area. Field testing and monitoring showed that after PCI remediation, the vibration acceleration decreased by 16.7% at the end of track slab and by 9.1% in the middle of track slab in 12 h; the deviator of the vertical track alignment was reduced from −9.58 mm to −0.08 mm in 3 days. A longer 6-month filed monitoring showed that the vertical track alignment deviator remained in a relatively low level (less than −0.62 mm) after PCI remediation, and there was no mud pumping reoccurrence in the PCI remediated area, indicating the performance of the proposed remediation method.