HARMONI is an integral field spectrograph working at visible and near-infrared wavelengths over a range of spatial scales from ground layer corrected to fully diffraction-limited. The instrument has been chosen to be part of the first-light complement at the European Extremely Large Telescope (E-ELT). This paper describes the instrument control electronics to be developed at IAC. The large size of the HARMONI instrument, its cryogenic operation, and the fact that it must operate with enhanced reliability is a challenge from the point of view of the control electronics design. The present paper describes a design proposal based on the current instrument requirements and intended to be fully compliant with the ESO E-ELT standards, as well as with the European EMC and safety standards. The modularity of the design and the use of COTS standard hardware will benefit the project in several aspects, as reduced costs, shorter schedule by the use of commercially available components, and improved quality by the use of well proven solutions.