In this paper, a performance comparison between sub-micron thick AlGaN/GaN and AlN/GaN HEMT devices are reported. Various gate lengths have been employed in order to analyze the impact on DC and RF performances. Electrical characteristics of these structures for 100 nm gate length show a higher maximum drain current, extrinsic transconductance Gm and RF performance with the AlN barrier as expected. An excellent electron confinement with a low leakage current below 10 µA/mm is achieved up to VDS = 30 V on both structures and can be combined with low trapping effects despite the thin total growth thickness of less than 1 µm on silicon. These results demonstrate the interest of sub-micron thick AlN/GaN-on-Si heterostructures for high frequency applications.