A soybean cultivar, designated SE90346, is disclosed. The invention relates to the seeds of soybean cultivar SE90346, to the plants of soybean SE90346 and to methods for producing a soybean plant produced by crossing the cultivar SE90346 with itself or another soybean variety. The invention further relates to hybrid soybean seeds and plants produced by crossing the cultivar SE90346 with another soybean cultivar.