X-ray fluorescence microtomography (μXFCT) is a nondestructive analytical technique and has been widely used to nondestructively detect and quantify the elemental composition and distributions in samples. Usually, synchrotron radiation X-rays are used for μXFCT, due to its high flux density. In this paper, a laboratory-source-based μXFCT system was developed, in which a polycapillary lens is employed to focus the X-ray beam and improve the flux density. The maximum likelihood expectation maximization algorithm was used to reconstruct the computed tomography slices at a limited number of projections. The experimental results demonstrated that the developed system could reveal the elemental distribution inside the test sample, with an elemental sensitivity of 1000 ppm.