An Organ-on-a-Chip (OoC) is a microfluidic device that mimics an organ function on a chip. The goal of the OoC technology is to create disease models of various organs and use them to minimise animal testing. One of the important parameters to maintain the cells/tissues on the OoC is the temperature, typically at 37 °C. Usually, cell culture incubators are used to maintain the temperature of cells on the OoC. However, it is inconvenient for external flow control instrumentation to interface with OoC inside the incubator, and other temperatures being not possible. Therefore, an on-chip temperature controller is needed. In this report, a temperature control system for an OoC is designed, implemented and tested. To cover a wide temperature range, multiple peltier elements are chosen to confine the temperature control only at the region close to cell chambers in the OoC. A resistive temperature detector (RTD) is used as feedback to control the temperature by a proportional-integral-derivative (PID) controller. To avoid any heat loss beyond the Organ-on-a-Chip, a 3D-printed polylactic acid (PLA) holder with good thermal insulating properties is used. The holder is designed for four chips to accommodate control chips along with test chips. A dedicated PCB with control electronics is designed and implemented to control the temperature on all four chips powered by a battery. A temperature uniformity of +/- 0.7 °C of 19 mm at 68 μL/min and 23 mm at 10 μL/min along a total microfluidic channel length of 40 mm (from inlet to outlet), a width of 5 mm, and a depth of 0.3 mm before compression, was achieved. The response time to recover from changes in the temperature is approximately 2 minutes. With a power consumption of 0.84 Watts per chip to maintain 37 °C, four chips can function on a 20000 mAh battery for a minimum of 4.5 hours (only cooling at a minimum of 18 °C) and a maximum of 8.3 hours (only heating at 37 °C) before recharge. The temperature control system was tested on Hepatocytes and Cholangiocytes for liver-on-a-chip applications, which showed that the oxygen disappearance rate is 9.87 times faster when maintained at 37 °C compared to room temperature.