In this paper, proposes a microwave brain imaging system to detect brain tumors using a metamaterial (MTM) loaded three-dimensional (3D) stacked wideband antenna array. The antenna is comprised of metamaterial-loaded with three substrate layers, including two air gaps. One 1 × 4 MTM array element is used in the top layer and middle layer, and one 3 × 2 MTM array element is used in the bottom layer. The MTM array elements in layers are utilized to enhance the performance concerning antenna's efficiency, bandwidth, realized gain, radiation directionality in free space and near the head model. The antenna is fabricated on cost-effective Rogers RT5880 and RO4350B substrate, and the optimized dimension of the antenna is 50 × 40 × 8.66 mm3. The measured results show that the antenna has a fractional bandwidth of 79.20% (1.37-3.16 GHz), 93% radiation efficiency, 98% high fidelity factor, 6.67 dBi gain, and adequate field penetration in the head tissue with a maximum of 0.0018 W/kg specific absorption rate. In addition, a 3D realistic tissue-mimicking head phantom is fabricated and measured to verify the performance of the antenna. Later, a nine-antenna array-based microwave brain imaging (MBI) system is implemented and investigated by using phantom model. After that, the scattering parameters are collected, analyzed, and then processed by the Iteratively Corrected delay-multiply-and-sum algorithm to detect and reconstruct the brain tumor images. The imaging results demonstrated that the implemented MBI system can successfully detect the target benign and malignant tumors with their locations inside the brain.