This work demonstrates a cost-effective manufacturing method of flexible and fully printed microheaters, using carbon nanotubes (CNTs) as the heating element. Two different structures with different number of CNT layers have been characterized in detail. The benchmarking has been carried out in terms of maximum operating temperature, as well as nominal resistance and input power for different applied voltages. Their performances have been compared with previous reports for similar devices, fabricated with other technologies. The results have shown that the heaters presented can achieve high temperatures in a small area at lower voltages and lower input power. In particular, the fully printed heaters fabricated on a flexible substrate covering an area of 3.2 mm2 and operating at 9.5 V exhibit a maximum temperature point above 70 °C with a power consumption below 200 mW. Therefore, we have demonstrated that this technology paves the way for a cost-effective large-scale fabrication of flexible microheaters aimed to be integrated in flexible sensors.