The QUIJOTE-CMB experiment has been described in previous publications. Here we describe the architecture of the control system, hardware and software, of the QUIJOTE I instrument (MFI). It is a multi-channel instrument with five separate polarimeters: two of which operate at 10-14 GHz, two of which operate at 16-20 GHz, and a central polarimeter at 26-36 GHz. Each polarimeter can rotate at a speed of up to 1 Hz and also can move to discrete angular positions which allow the linear polar parameters Q, U and I to be derived. The instrument is installed in an alt-azimuth telescope which implements several operational modes: movement around the azimuth axis at a constant velocity while the elevation axis is held at a fixed elevation; tracking of a sky object; and raster of a rectangular area both in horizontal and sky coordinates. The control system of both, telescope and instrument, is based in the following technologies: an LXI-VXI bus is used for the signal acquisition system; an EtherCAT bus implements software PLCs developed in TwinCAT to perform the movement of the 5 polarimeters and the 2 axes of the telescope. Science signal, angular positions of the 5 polarimeters and telescope coordinates are sampled at up to 4000 Hz. All these data are correlated by a time stamp obtained from an external GPS clock implementing the Precise Time Protocol-1588 which provides synchronization to less than 1 microsecond. The control software also acquires housekeeping (HK) from the different subsystems. LabVIEW implements the instrument user interface.