The notion of thermophoretic particle deposition is used in a number of applications, including thermal exchanger walls. It is important to identify the transport processes in action in systems such as thermal precipitators, exhaust devices, optical transmission fabrication processes, and so on. Based on these application points of view, the present work studies the performance of nanoparticle aggregation stagnation point flow over a rotating sphere during the occurrence of thermophoretic particle deposition. The nonlinear governing equations are transformed into the ordinary differential equation by utilizing suitable similarity variables. The numerical outcomes of the reduced equations along with boundary conditions are solved by the Runge–Kutta–Fehlberg 45 (RKF-45) order method with shooting procedure. The numerical results are shown with the assistance of graphs. The impacts of various dimensionless constraints on velocity, thermal, and concentration profiles are studied under the occurrence and absence of nanoparticle aggregation. The study reveals that the primary velocity is enhanced with increasing values of the acceleration parameter, but secondary velocity diminishes. The impressions of the rotation parameter will improve the primary velocity. The concentration profiles will diminish with an improvement in the thermophoretic parameter. The surface drag force is greater in nanoparticles with aggregation than nanoparticles without aggregation in the Cfx case but a reverse behavior is seen in the Cfz case. Further, the rate of heat distribution increases with a rise in the solid volume fraction, whereas the rate of mass distribution grows as the thermophoretic parameter grows.