A new butt joining method for ceramics by microwave heating was developed. Ceramics were heated in a rectangular cavity, and a klystron of maximum 3 kW at 6 GHz was used as the power amplifier. The heating system can control an iris, a plunger, and the microwave power to maintain the power efficiency up to 90% and the accuracy within ±10°C at 1800 °C. This system was applied to alumina-alumina direct joining. The average strength of alumina rods (92% purity) joined for 3 min was 420 MPa, which was equal to the original strength. The joined boundary line at the interface was not observed, and there was little difference in microstructure between before and after joining. This suggests that sintering aids in the grain boundary phase were preferentially heated and melted, resulting in the sound joining of ceramics. Next, silicon nitride ceramics containing yttrium were indirectly joined with an intermediate, which was a sintered ceramic sheet having lower purity and larger dielectric loss factor than the base material. The microwave energy was concentrated on the ceramic sheet, so that only the joining area was locally heated. The strength of the joined rods was in excess of 70% of the base material, but a deficient layer of yttrium occurred in the area of the joined boundary.