Crohn’s disease (CD) is a chronic idiopathic inflammatory bowel condition that can affect any part of the gastrointestinal tract. Several hundred candidate loci or genes including _PTPN2_ have been reportedly associated with CD. A whole-exome sequencing (WES) was conducted in a 9-year-old Lebanese girl with a CD onset at 13 months and in both her asymptomatic parents. The analysis detected an extremely rare homozygous variant in _PTPN2_: c.359C>T, p.(Ser120Leu) in the patient, while both her parents were heterozygous. This variant, located in the protein tyrosine phosphatase (PTP) domain within a highly conserved amino acid, is classified as VUS according to the American College of Medical Genetics (ACMG) criteria. To evaluate the hypothetical functional consequences of the identified variant, a quantitative expression analysis of _PTPN2_ was performed in blood tissues of the patient, her parents, and two healthy controls. _PTPN2_ expression was not noted in the patient compared to her parents and the normal controls, suggesting a functional _PTPN2_ impairment caused by c.359C>T. This variant c.359C>T, p.(Ser120Leu) in _PTPN2_ has never been previously described in the literature. Our report suggests an association of _PTPN2_: c.359C>T with early-onset CD.