The density functional theory (DFT) based on the bridge density functional and the fundamental-measure theory (FMT) have been used to investigate the structural properties of one- and two-component penetrable spheres in a spherical pore. The Monte Carlo simulations have been carried out to compare with the theoretical results. The result shows that at low temperature the FMT functional is better than the DFT based on the bridge density functional and compares well with the computer simulations. At high temperature the DFT based on the bridge density functional is better than the FMT functional. These results suggest the reliable accuracy of the modified Verlet closure for the penetrable spheres at high temperature. However, the accuracy of both the FMT functional and the DFT based on the bridge density functional deteriorates if the packing fraction is increased.