Many sensitive atomic devices require magnetic shield to reduce external magnetic field interference. Mn–Zn ferrites are optimistic candidates for shielding because they provide a high shielding factor and a low magnetic noise. This study evaluated the magnetic noise of Mn–Zn ferrite magnetic shield based on its grain size. The morphologies of Mn–Zn ferrite samples were characterized to establish a correlation between their grain sizes and magnetic permeability, which can be used to calculate magnetic noises. The correlation was then used to evaluate the shielding performance of another Mn–Zn ferrite, where the magnetic noise of the magnetic shield made from the ferrite was calculated to be 2.53 f−1/2fT. The magnetic noise of the magnetic shield was also measured experimentally using a spin-exchange relaxation-free atomic magnetometer. The measured magnetic noise of ferrite shield was 2.61 f−1/2fT, while the white noise of the atomic magnetometer was 0.71 fT/Hz1/2 below 100 Hz. The consistency between the experimental results and predicted values suggests the viability of the proposed approach, providing a convenient, efficient, and precise method for developing ferrite ceramics materials for low-noise magnetic shields.