Eddy current transducer with sensing coils placed orthogonally and connected in differential mode was introduced to evaluate fatigue cracks in clad pipeline circumferential welds. A dedicated embedded electronic hardware was developed to drive the transducer and measure the electrical complex impedance of the coils, and was specifically designed for operation under autonomous in-line inspection tool. In the laboratory experiments, an automated inspection was performed with the goal to evaluate transducer’s detectability, and different scanning speed was tested to reproduce in service situation. The results have confirmed that the introduced eddy current transducer is a potential solution for fatigue crack detection in clad circumferential weld root, while the hardware developed presented a reasonable SNR reaching the data rate required to be incorporated in an autonomous in-line inspection tool.