Micro-CT scanning has become an accepted standard for anatomical imaging in small animal disease and genome mutation models. Concurrently, perfusion imaging via tracking contrast dynamics after injection of an iodinated contrast agent is a well-established tool for clinical CT scanners. However, perfusion imaging is not yet commercially available on the micro-CT platform due to limitations in both radiation dose and temporal resolution. Recent hardware developments in micro-CT scanners enable continuous imaging of a given volume through the use of a slip-ring gantry. Now that dynamic CT imaging is feasible, data may be acquired to measure tissue perfusion using a micro-CT scanner (CT Imaging, Erlangen, Germany). However, rapid imaging using micro-CT scanners leads to high image noise in individual time frames. Using the standard filtered backprojection (FBP) image reconstruction, images are prohibitively noisy for calculation of voxel-by-voxel perfusion maps. In this study, we apply prior image constrained compressed sensing (PICCS) to reconstruct images with significantly lower noise variance. In perfusion phantom experiments performed on a micro-CT scanner, the PICCS reconstruction enabled a reduction to 1/16 of the noise variance of standard FBP reconstruction, without compromising the spatial or temporal resolution. This enables a significant increase in dose efficiency, and thus, significantly less exposure time is needed to acquire images amenable to perfusion processing. This reduction in required irradiation time enables voxel-by-voxel perfusion maps to be generated on micro-CT scanners. Sample perfusion maps using a deconvolution-based perfusion analysis are included to demonstrate the improvement in image quality using the PICCS algorithm.