In recent years, the emergence of nanotechnology experienced incredible development in the field of medical sciences. During the past decade, investigating the characteristics of nanoparticles during fluid flow has been one of the intriguing issues. Nanoparticle distribution and uniformity have emerged as substantial criteria in both medical and engineering applications. Adverse effects of chemotherapy on healthy tissues are known to be a significant concern during cancer therapy. A novel treatment method of magnetic drug targeting (MDT) has emerged as a promising topical cancer treatment along with some attractive advantages of improving efficacy, fewer side effects, and reduce drug dose. During magnetic drug targeting, the appropriate movement of nanoparticles (magnetic) as carriers is essential for the therapeutic process in the blood clot removal, infection treatment, and tumor cell treatment. In this study, we have numerically investigated the behavior of an unsteady blood flow infused with magnetic nanoparticles during MDT under the influence of a uniform external magnetic field in a micro-tube. An optimal homotopy asymptotic method (OHAM) is employed to compute the governing equation for unsteady electromagnetohydrodynamics flow. The influence of Hartmann number (Ha), particle mass parameter (G), particle concentration parameter (R), and electro-osmotic parameter (k) is investigated on the velocity of magnetic nanoparticles and blood flow. Results obtained show that the electro-osmotic parameter, along with Hartmann’s number, dramatically affects the velocity of magnetic nanoparticles, blood flow velocity, and flow rate. Moreover, results also reveal that at a higher Hartman number, homogeneity in nanoparticles distribution improved considerably. The particle concentration and mass parameters effectively influence the capturing effect on nanoparticles in the blood flow using a micro-tube for magnetic drug targeting. Lastly, investigation also indicates that the OHAM analysis is efficient and quick to handle the system of nonlinear equations.