Temperature control is vital in micro-heaters used in medical devices such as the polymerase chain reaction (PCR). The primary goal is to achieve tight control and a high rate of heating for a portable, low-cost medical device. Even though the fact that several designs for micro-heaters have been proposed, uniform temperature distribution and the high-speed heating rate remain challenging for micro-heaters. This high speed is achieved by the reduction of the thermal mass. The most common methods for reducing thermal mass or heating time in a device are to establish a highly desired structural design and to select a better heating mechanism with a robust controller. Increasing the thermal mass improves temperature distribution on the heater surface but slows heat transfer. On the other hand, removing the thermal mass makes the controller struggle to provide a high-temperature uniformity distribution on the micro-heater surface. In this study, we provide a design of a cost-effective, high-speed, thin-film micro-heater based on the Joule heating technique. The CoventorWare software tool is used to simulate the temperature distribution of the micro-heater. The heater provides a well-distributed temperature on the heated surface. When a DC voltage of 24 V was applied for 250 s, a maximum temperature of 272 °C was obtained. Besides, the heater's average heating rate is 15 °C/s. The heater is then fabricated with the micro-electromechanical systems (MEMS) technology on a silicon substrate. The transfer function of the heating system is computed. Two controllers are designed to control the temperature of the micro-heater and improve its response. The classical proportional-integral-derivative (PID) controller produces rise time (Tr) of 21.9 s, settling time (Ts) of 73.3 s, and a maximum overshoot (Mp) of 4.8 %. Then by applying a fractional-order proportional-integral-derivative (FOPID) controller, a great enhancement in the system performance is observed, the controller is faster than the normal PID controller, the rise time (Tr) reaches 16.4 s and the settling time (Ts) reaches 23.6 s. It also reduces the maximum overshoot (Mp) to 0.32 %.