Cylindrical ferrite shields consisting of multiple annuli can provide low-magnetic-noise environments. However, the gaps between different parts of the shield adversely affect the shielding performance. In this study, we numerically study the influence of the gaps on both the axial and radial magnetic noise of the multi-annular ferrite shield with different gap widths, permeabilities, and aspect ratios using the generalized Nyquist relation and the finite element method. Our study indicates that as the gap width increases, the axial magnetic noise decreases, while the radial magnetic noise increases. For the shield with a gap width of 0.10 mm and an aspect ratio of one in our study, the axial magnetic noise decreases by 5.2%, and the radial magnetic noise increases by 8.3%–33.5%. The difference in the increase is related to the permeability, and gaps have smaller effect on the radial magnetic noise of the shield with lower permeabilities. Therefore, compared with the no-gap shield, the multi-annular ferrite shield can provide an even better low-magnetic-noise environment along the axial direction. Although the gaps can induce an increase of the radial magnetic noise, this detrimental effect can be suppressed significantly by using a ferrite material with lower permeability and reducing the gap width. Our findings can aid in the application and optimization of low-noise ferrite shields.