Optical isolators provide one-way propagation and are necessary to protect laser diodes from damage and unstable operation caused by reflected light. Although magneto-optical (MO) devices can operate as isolators, achieving high-density integration using conventional direct bonding methods is difficult because a large and thick growth substrate remains on the circuits. We experimentally demonstrated a compact Mach-Zehnder interferometer-based MO isolator with Si waveguides by the µ-transfer printing of a Ce:YIG/SGGG coupon. The isolator has a footprint of 0.25 mm2 with a Ce:YIG/SGGG coupon of 50 × 800 µm2 and ∼ 1-µm thickness and achieved a maximum isolation ratio of 14 dB in telecom bands.