The shape of magnetically shielded room (MSR) has been designed by using a numerical method for 3-D magnetic field analysis taking into account eddy currents. in which the finite element method is employed. Firstly, 3-D magnetic field distribution in MSR is computed to investigate an optimal shape. A spatial distribution of a MSR with a rectangular tube is compared with that without a tube. Secondly, results computed are verified by comparing with those measured in an actually constructed MSR. The spatial magnetic field distribution obtained by using the 3-D analysis is roughly in agreement with those measured, especially when magnetic noise of 1Hz is applied. The rectangular tube is effective to make the magnetic field distribution uniform in region of interest of MSR for measuring extremely weak magnetic fields.