Microfluidic organ-on-a-chip (OoC) technology has enabled studies on dynamic physiological conditions as well as being deployed in drug testing applications. A microfluidic pump is an essential component to perform perfusion cell culture in OoC devices. However, it is challenging to have a single pump that can fulfil both the customization function needed to mimic a myriad of physiological flow rates and profiles found in vivo and multiplexing requirements (i.e., low cost, small footprint) for drug testing operations. The advent of 3D printing technology and open-source programmable electronic controllers presents an opportunity to democratize the fabrication of mini-peristaltic pumps suitable for microfluidic applications at a fraction of the cost of commercial microfluidic pumps. However, existing 3D-printed peristaltic pumps have mainly focused on demonstrating the feasibility of using 3D printing to fabricate the structural components of the pump and neglected user experience and customization capability. Here, we present a user-centric programmable 3D-printed mini-peristaltic pump with a compact design and low manufacturing cost (~USD 175) suitable for perfusion OoC culture applications. The pump consists of a user-friendly, wired electronic module that controls the operation of a peristaltic pump module. The peristaltic pump module comprises an air-sealed stepper motor connected to a 3D-printed peristaltic assembly, which can withstand the high-humidity environment of a cell culture incubator. We demonstrated that this pump allows users to either program the electronic module or use different-sized tubing to deliver a wide range of flow rates and flow profiles. The pump also has multiplexing capability as it can accommodate multiple tubing. The performance and user-friendliness of this low-cost, compact pump can be easily deployed for various OoC applications.