This article studies the optimal design approach for a portable nuclear magnetic resonance (NMR) system for use in non-destructive flow measurement applications. The mechanical and electromagnetic design procedures were carried out using the Ansys Maxwell finite-element analysis (FEA) software tool. The proposed procedure considered homogeneity and strength constraints while ensuring the desired functionality of the intended device for a given application. A modified particle swarm optimization (MPSO) algorithm was proposed as a reference design framework for optimization stages. The optimally designed NMR tool was prototyped, and its functionality was validated via several case studies. To assess the functionality of the prototyped device, Larmor frequency for hydrogen atom was captured and compared with theoretical results. Furthermore, the functionality and accuracy of the prototyped NMR tool is compared to the off-the-shelf NMR tool. Results demonstrated the feasibility and accuracy of the prototyped NMR tool constrained by factors, such as being lightweight and compact.