Magnetic resonance imaging (MRI) scanners have recently been used for magnetic actuation of robots for minimally invasive medical operations. Due to MRI's high soft‐tissue selectivity, it is possible to obtain 3D images of hard‐to‐reach cavities in the human body, where the wireless miniature magnetic robots powered by MRI could be employed for high‐precision targeted operations, such as drug delivery, stem cell therapy, and hyperthermia. However, the state‐of‐the‐art fast magnetic robot‐tracking methods in MRI are limited above millimeter‐size scale, which restricts the potential target regions inside the human body. Herein, a fast 1D projection‐based MRI approach that can track magnetic particles down to 300 μm diameter (1.17 × 10−2 emu) is reported. The technique reduces the trackable magnetic particle size in MRI‐powered navigation fivefold compared with the previous fast‐tracking methods. A closed‐loop MRI‐powered navigation with 0.78 ± 0.03 mm trajectory‐following accuracy in millimeter‐sized in vitro 2D channels and a 3D cavity setup using the tracking method is demonstrated. Furthermore, the feasibility of submillimeter magnetic robot tracking in ex vivo pig kidneys (N = 2) with a 3.6 ± 1.1 mm accuracy is demonstrated. Such a fast submillimeter‐scale mobile robot‐tracking approach can unlock new opportunities in minimally invasive medical operations.