A hybrid approach consisting of a Markovian fluctuating hydrodynamics of the fluid and a non-Markovian Langevin dynamics with the Ornstein–Uhlenbeck noise perturbing the translational and rotational equations of motion of a nanoparticle is employed to study the thermal motion of a nearly neutrally buoyant nanoparticle in an incompressible Newtonian fluid medium. A direct numerical simulation adopting an arbitrary Lagrangian–Eulerian based finite element method is employed for the simulation of the hybrid approach. The instantaneous flow around the particle and the particle motion are fully resolved. The numerical results show that (a) the calculated temperature of the nearly neutrally buoyant Brownian particle in a quiescent fluid satisfies the equipartition theorem; (b) the translational and rotational decay of the velocity autocorrelation functions result in algebraic tails, over long time; (c) the translational and rotational mean square displacements of the particle obey Stokes–Einstein and Stokes–Einstein–Debye relations, respectively; and (d) the parallel and perpendicular diffusivities of the particle closer to the wall are consistent with the analytical results, where available. The study has important implications for designing nanocarriers for targeted drug delivery. A major advantage of our novel hybrid approach employed in this paper as compared to either the fluctuating hydrodynamics approach or the generalized Langevin approach by itself is that only the hybrid method has been shown to simultaneously preserve both hydrodynamic correlations and equilibrium statistics in the incompressible limit.