In modern printed electronics, the performances of a circuit and a device are severely deteriorated by the electromagnetic noise in the gigahertz (GHz) frequency range, such as the simultaneous switching noise and ground bounce noise. A compact and multi-stack electromagnetic bandgap (CMS-EBG) structure is proposed to suppress the electromagnetic noise over the GHz frequency range with a short distance between a noise source and a victim on multilayer printed circuit boards (MPCBs). The original configuration of the stepped impedance resonators is presented to efficiently form multiple stacks of EBG cells. The noise suppression characteristics of the CMS-EBG structure are rigorously examined using Floquet-Bloch analysis. In the analysis, dispersion diagrams are extracted from an equivalent circuit model and a full-wave simulation model. It is experimentally verified that the CMS-EBG structure suppresses the resonant modes over the wideband frequency range with a short source-to-victim distance; thus, this structure substantially mitigates GHz electromagnetic noise in compact MPCBs.