In this paper, we present an optimized FPGA implementation of a novel, fast and highly parallelized NTTbased polynomial multiplier architecture, which proves to be effective as an accelerator for lattice-based homomorphic cryptographic schemes. As I/O operations are as time-consuming as NTT operations during homomorphic computations in a host processor/accelerator setting, instead of achieving the fastest NTT implementation possible on the target FPGA, we focus on a balanced time performance between the NTT and I/O operations. Even with this goal, we achieved the fastest NTT implementation in literature, to the best of our knowledge. For proof of concept, we utilize our architecture in a framework for Fan-Vercauteren (FV) homomorphic encryption scheme, utilizing a hardware/software co-design approach, in which polynomial multiplication operations are offloaded to the accelerator via PCIe bus while the rest of operations in the FV scheme are executed in software running on an off-the-shelf desktop computer. Specifically, our framework is optimized to accelerate Simple Encrypted Arithmetic Library (SEAL), developed by the Cryptography Research Group at Microsoft Research [1], for the FV encryption scheme, where large degree polynomial multiplications are utilized extensively. The hardware part of the proposed framework targets Xilinx Virtex-7 FPGA device and the proposed framework achieves almost 11x latency speedup for the offloaded operations compared to their pure software implementations. We achieved a throughput of almost 800K polynomial multiplications per second, for polynomials of degree 1024 with 32-bit coefficients.