Gas foil bearings (GFBs) have many noticeable advantages over the conventional rigid gas bearings, such as frictional damping of the compliance structure and tolerance to the rotor misalignment, so they have been successfully adopted as the key element that makes possible oil-free turbomachinery. As the adoption of the GFB increases, one of the critical elements for its successful implementation is thermal management. Even though heat generation inside the GFB is small due to the low viscosity of the lubricant, many researchers have reported that the system might fail without an appropriate cooling mechanism. The objective of the current research is to demonstrate the reliability of GFBs installed in the hot section of a micro-gas turbine (MGT). For the cooling of the GFBs, we designed a secondary flow passage and thermohydrodynamic (THD) analysis has been done for temperature prediction. In the analysis, the 3D THD model for the radial GFB extended to include the surrounding structure, such as the plenum, chamber, and the rotor in the solution domain by solving global mass and energy balance equations. In the MGT, the pressurized air discharged from the compressor wheel was used as the cooling air source, and it was injected into the plenum between two radial GFBs. We monitored the pressure and temperature of the cooling air along the secondary flow passage during the MGT operation. No thermal instability occurred up to the maximum operation speed of 43,000 rpm. The test results also showed that the pressure drop between the main reservoir and the plenum increases with an increasing operation speed, which indicated an increased cooling air flow into the plenum. The plenum and bearing sleeve temperature was maintained close to the cooling air source temperature for the entire speed due to a sufficient cooling air flow into the bearing. In addition, the direct injection of the cooling air from the main stream lowered the bearing sleeve temperature by 5–20 °C over the injection through the reservoirs. The predicted plenum and bearing sleeve temperatures with the developed THD model show good agreement with the test data.