Rubella is a viral disease that can lead to severe health complications, especially in pregnant women and their unborn babies. Understanding the dynamics of the Rubella disease model is crucial for developing effective strategies to control its spread. This paper introduces a major innovation by employing a novel piecewise approach that incorporates two different kernels. This innovative approach significantly enhances the accuracy of modeling Rubella disease dynamics. In the first interval, the Caputo operator is employed to address initial conditions, while the Atangana–Baleanu derivative is utilized in the second interval to account for anomalous diffusion processes. A thorough theoretical analysis of the piecewise derivative for the problem is provided, discussing mathematical properties, stability, and convergence. To solve the proposed problem effectively, the piecewise numerical Newton polynomial technique is employed and the numerical scheme for both kernels is established. Through extensive numerical simulations with various fractional orders, the paper demonstrates the approach’s effectiveness and flexibility in modeling the spread of the Rubella virus. Furthermore, to validate the findings, the simulated results are compared with real data obtained from Rubella outbreaks in Uganda and Tanzania, confirming the practical relevance and accuracy of this innovative model.