The rates of atomic clustering and precipitation hardening are closely related to the diffusivity of solutes and the concentration of vacancies during the natural aging of aluminum alloys. The measurement of the diffusivity of solutes at room temperature, especially in systems with an equilibrium vacancy concentration, is beneficial to the design of the aging process. However, this measurement has long been challenging because of the extremely low diffusion rates of solutes in aluminum at room temperature and the presence of supersaturated vacancies. In this work, we propose a method to quantify the diffusivity of solutes based on the kinetic evaluation of the spinodal decomposition process. This evaluation involves conducting atom probe tomography experiments, analyzing the radial distribution function, and modeling the phase separation process using the Cahn–Hilliard theory. The aging experiments were conducted on nanoscale samples, where excess vacancies can be eliminated at free surfaces due to a high surface-to-volume ratio. The results yielded a diffusivity of Zn in the Al-12.5 at.% Zn alloy of (1.32 ± 0.46) × 10$^{−25}$ m$^2$/s at 295 K. This work introduces a novel approach to assess the solute diffusivity under conditions of equilibrium vacancy concentration at room temperature and expands the temperature range for measuring the diffusivity in systems with spinodal decomposition, particularly in cases where kinetic data at low temperatures are scarce.