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Abstract We first propose an ultra-compact energy-efficient time-domain vector-by-matrix multiplier (VMM) based on commercial 3D-NAND flash memory structure. The proposed 3D-VMM uses a novel resistive successive integrate and re-scaling (RSIR) scheme to eliminate the stringent requirement of a bulky load capacitor which otherwise dominates the area- and energy-landscape of the conventional time-domain VMMs. Our rigorous analysis, performed at the 55 nm technology node, shows that RSIR-3D-VMM achieves a record-breaking area efficiency of ∼0.02 μ m 2 /Byte and the energy efficiency of ∼6 f J/Op for a 500 × 500 4-bit VMM, representing 5× and 1.3× improvements over the previously reported 3D-VMM approach. Moreover, unlike the previous approach, the proposed VMM can be efficiently tailored to work in a smaller current output range. Our second major contribution is the development of 3D-aCortex, a multi-purpose neuromorphic inference processor that utilizes the proposed 3D-VMM block as its core processing unit. Rigorous performance modeling of the 3D-aCortex targeting several state-of-the-art neural network benchmarks has shown that it may provide a record-breaking 30.7 MB mm −2 storage efficiency, 113.3 TOp/J peak energy efficiency, and 10.66 TOp/s computational throughput. The system-level analysis indicates that the gain in the area-efficiency of RSIR leads to a smaller data transfer delay, which compensates for the reduction in the VMM throughput due to an increased input time window.