According to the invention, there is provided a novel soybean variety, designated XB39J04. This invention thus relates to the seeds of soybean variety XB39J04, to the plants of soybean XB39J04, to plant parts of soybean variety XB39J04 and to methods for producing a soybean plant produced by crossing soybean variety XB39J04 with another soybean plant, using XB39J04 as either the male or the female parent. This invention also relates to methods for introgressing a transgenic or mutant trait into soybean variety XB39J04 and to the soybean plants and plant parts produced by those methods. This invention also relates to soybean varieties or breeding varieties and plant parts derived from soybean variety XB39J04, to methods for producing other soybean varieties or plant parts derived from soybean variety XB39J04 and to the soybean plants, varieties, and their parts derived from use of those methods. This invention further relates to soybean seeds, plants, and plant parts produced by crossing the soybean variety XB39J04 with another soybean variety.