In the focusing system design of an infrared(IR) imager, the motor drives the focusing lens group to reciprocate along the linear guide rail to change the position of the focusing lens group accurately and to change the focal length. To control the position of the focus lens group accurately, the focus control system requires a high-resolution encoder to reflect the position of the focus lens group to realize closed-loop control of the group. In the focusing control system of the IR imager, an incremental encoder is used to feedback the position of the focusing lens group. According to the characteristics of the incremental encoder, because of the rich logic resources and programmable flexibility of the complex programmable logic device, a readout circuit is designed that can accurately feedback the position of the focusing lens group in real time. Verification in an actual project demonstrated that this scheme can read out the position of the incremental encoder accurately in real time, has reliable anti-interference ability, and meets the system requirements of high-precision position control.