Mutations including nonsense mutations, missense mutations, splicing-site mutations, insertions, and deletions in phosphate regulating genes on the X-chromosome (PHEX) are known to be responsible for X-linked hypophosphatemic rickets. The PHEX gene encodes an endopeptidase that is involved in phosphate regulation. Herein we present a female patient with sporadic hypophosphatemic rickets harboring a novel deletion mutation (c.1586_1586+1delAG; p.Glu529GlyfsX41) at exon 14 and intron 14 junction, which caused a premature termination at codon 569 and possibly produced a truncated PHEX protein. The laboratory and radiologic findings of the patient are reviewed to correlate the impact of the two-base deletion mutations at the exon-intron junction.