Paper has attracted significant attention recently as a microfluidic component and platform, especially in passive pumping devices due to its porous and uniform absorbing nature. Many investigations on 1D and 2D fluid flows were carried out. However, no experimental work has been reported on the three-dimensional effect in porous geometry to improve pumping characteristics in microchannels. Therefore, in this study, the fluid flow in 3D paper-based passive pumps was investigated in microchannels using cylindrical pumps. The effect of pump diameter, porosity, and programmability was investigated to achieve desired flow variations. The results indicated that the flow rate of water increased with an increase in the diameter and porosity of paper pumps. Maximum flow rates achieved for 14 mm diameter pumps of 0.5 and 0.7 porosities were 5.29 mm3/s (317.4 μl/min) and 6.97 mm3/s (418.2 μl/min), respectively. The total volume of fluid imbibition ranged between 266 and 567 μl for 8 and 14 mm diameter pumps, respectively. Moreover, 3D passive pumps can transport larger volumes of liquid with an improved flow rate, programmability, and control, in addition to being inexpensive and simple to design and fabricate. Most importantly, a single 3D paper pump showed an increasing, decreasing, and constant flow rate all in a single microchannel. With these benefits, the passive pumps can further improve the pumping characteristics of microfluidic platforms enabling a cost effective and programmable point-of-care diagnostic device.