The pulsed quadrupole magnets have been installed in KEKB for the betatron tune adjustment. These magnets need to be controlled by the existing EPICS-based control system of the KEKB accelerator. While the control logic required for the operation of the magnet power supplies is rather conventional, it is preferable that we choose a front-end controller which allows us to develop and maintain the software in a highly efficient manner to cope with limited human resources. In order to satisfy this requirement, a new type of Input / Output Controller (IOC), which runs Linux on a CPU module of FA-M3 Programmable Logic Controller (PLC), has been adopted. The CPU functions with normal I/O modules of FA-M3 on the PLC-bus. We found that replacing ladder programs with EPICS sequencer makes the development and maintenance of the software for the IOC considerably efficient. This paper describes the details of the new IOC and its experiences in KEKB operation including long term stability.