Molecular characterization of leaf development has not been well studied in soybean. Two soybean isolines that differed in leaf phenotype were profiled by high throughput RNA sequencing. A Clark isoline homozygous for a dominant mutant allele, Lf1, that specifies a five-foliate compound leaf was compared to wild type Clark that is homozygous for the standard allele that produces trifoliate leaves. Although Lf1 is dominant it presents variable expressivity as the young plantlets with the Lf1Lf1 genotype initially have trifoliate leaves in the first few weeks after which they transition to five-foliate leaves. At later developmental stages, they begin to produce four-foliate or trifoliate leaves. A total of 91.4 and 94.7 million reads were generated in each lane of Illumina sequencing for the wild type and five-foliate-mutant libraries, respectively. Of these, 65.4 (71%) and 65 (68.6%) million reads aligned to the 78,743 target Glyma models from the reference soybean genome (cv. Williams 82) with maximum of 3 mismatches and up to 25 alignments. The comparative studies of the transcript profiles of the wild-type versus mutant line revealed a number of differentially expressed genes including many transcription factors. A total of 1,297 and 2,083 genes were up-regulated in the wild type and five-foliate mutant, respectively, that showed ≥2-fold expression difference. This study provides insight into the initial understanding of leaf development in soybean by revealing a number of genes differentially expressed between the wild type and five-foliate mutant. Perhaps some of these genes may be candidates for compound leaf development in soybean.