In current rail defect detection, ultrasonic testing from the rail head surface has the problem of the side of the rail bottom becoming a shadow zone. Therefore, as a method for detecting defects on the side of the rail bottom, we proposed a new defect detection system focusing on changes in magnetic flux leakage caused by the presence or absence of defects using a non-contact sensor placed above the side of the rail bottom and conducted a basic study through indoor tests. A coil to generate a magnetic field was installed on the rail head surface, and a magnetic sensor to measure the magnetic field was placed above the side of the rail bottom. The output of the magnetic sensor around the artificial defects created on the side of the rail bottom was assessed. As a result, it was suggested that the presence or absence of defects and the depth of the defects could be determined by changes in the magnetic sensor output in the absence of rail fastening systems. Furthermore, it was observed that even when the rail was secured with rail fastening systems, the presence of defects could be determined by changes in the magnetic sensor output.