We apply time-of-flight secondary ion mass spectroscopy (ToF-SIMS) and cross-sectioned trilayer samples to separately measure nanoparticle (NP) and polymer diffusion on micrometer length scales in polymer melts. We fabricate polymer/ diffusing medium/polymer trilayer samples and measure the cross section to extract the NP or deuterated polymer distribution in 3D using ToF-SIMS. After correcting the data for sample tilt, deconvoluting the beam resolution, and integrating the data to extract 1D concentration profiles, we fit the data to extract the diffusion coefficient. These results from cross-sectional ToF-SIMS are in excellent agreement with earlier studies using well-established ion beam methods. This work establishes ToF-SIMS as a reliable tool for measuring NP and polymer diffusion coefficients and opens the door to investigating diffusion in more complex polymer systems and across longer time and length scales.