A non-invasive, low-powered, and portable electromagnetic (EM) head imaging system is presented using metamaterial (MTM) loaded compact directional 3D antenna. The antenna consists of two slotted dipole elements with 2×3 and 3×3 finite MTM array elements in top and ground, respectively, and folded parasitic elements that operate within the frequency range of 1.12 GHz to 2.5 GHz. The MTM array elements are optimized to enhance the overall performance regarding antenna bandwidth, realized gain, efficiency, and directionality in both free space and proximity to the head model. The mathematical modelling is also analyzed to justify the integration of MTM unit cells to the top and ground side of the antenna. The impact of MTM on SAR analysis is also performed. A tissue-mimicking 3D head phantom is fabricated and measured to validate the antenna performance. A nine-antenna portable setup is used with the fabricated phantom to measure and collect the scattering parameters that are later analyzed to detect and reconstruct the haemorrhage images by applying the updated IC-CF-DMAS algorithm. The overall performance demonstrates the feasibility of the proposed system as a portable platform to successfully detect, locate and monitor the haemorrhages inside the head in EM imaging system.