The invention relates to the soybean variety designated 01046401. Provided by the invention are the seeds, plants and derivatives of the soybean variety 01046401. Also provided by the invention are tissue cultures of the soybean variety 01046401 and the plants regenerated therefrom. Still further provided by the invention are methods for producing soybean plants by crossing the soybean variety 01046401 with itself or another soybean variety and plants produced by such methods.