The Cherenkov Telescope Array (CTA) will be the leading ground-base observatory for Very High Energy (VHE) γ-ray astronomy for the next decades. Its southern site will host about 70 Small Sized Telescopes (SSTs) which will determine the CTA sensitivity at γ-ray energies between 1 and 300 TeV. One of the design options for the SST cameras is the silicon photomultiplier-based Compact High-Energy Camera (CHEC-S). The back-end electronics (BEE) of CHEC-S interconnects the camera front-end modules, provides power and clock distribution, aggregation, routing and timestamping of data and most importantly it implements the camera trigger system. A novel technique to tag muons using the capabilities of this system has been developed, studying and comparing different algorithms such as circle fitting, machine learning and simple pixel counting. This contribution describes the design of the CHEC-S BEE, and presents the results of the performance of this muon tagger, its on telescope integration tests, and the prospects of using it for other Cherenkov Telescopes types of CTA.