Amelogenin undergoes self-assembly and plays an essential role in guiding enamel mineral formation. The leucine-rich amelogenin peptide (LRAP) is an alternative splice product of the amelogenin gene and is composed of the N terminus (containing the only phosphate group) and the C terminus of full-length amelogenin. This study was conducted to investigate further the role of phosphorylation in LRAP self-assembly in the presence and absence of calcium using small angle X-ray scattering (SAXS). Consistent with our previous dynamic light-scattering findings for phosphorylated (+P) and non-phosphorylated (−P) LRAP, SAXS analyses revealed radii of gyration (Rg) for LRAP(−P) (46.3–48.0 Å) that were larger than those for LRAP(+P) (25.0–27.4 Å) at pH 7.4. However, added calcium (up to 2.5 mM) induced significant increases in the Rg of LRAP(+P) (up to 46.4 Å), while it had relatively little effect on LRAP(−P) particle size. Furthermore, SAXS analyses suggested compact folded structures for LRAP(−P) in the presence and absence of calcium, whereas the conformation of LRAP(+P) changed from an unfolded structure to a more compact structure upon the addition of calcium. We conclude that the single phosphate group in LRAP(+P) induces functionally important conformational changes, suggesting that phosphorylation may also influence amelogenin conformation and protein–mineral interactions during the early stages of amelogenesis.