A calcium (Ca)-deficient hydroxyapatite was investigated for its potential to remove Sr2+ from environmentally relevant water. We conducted sorption tests on solutions containing magnesium ion (Mg2+) and calcium ion (Ca2+) as competing cations at a strontium ion (Sr2+) concentration of 0.05 mmol/L. The Ca-deficient hydroxyapatite maintained a high Sr2+ sorption ratio of above 80% in the presence of Mg2+ and Ca2+ at the concentrations between 0.1 and 1.0 mmol/L, whereas the stoichiometric hydroxyapatite showed a lower ratio even in the presence of small amounts of Mg2+ and Ca2+ (72% for Mg2+ and 51% for Ca2+ at 0.1 mmol/L). For solutions with various Sr2+ concentrations between 0.01 and 10 mmol/L, Ca-deficient hydroxyapatite exhibited a higher Sr2+ sorption ratio than stoichiometric hydroxyapatite. The bonding states of Sr2+ on the Ca-deficient hydroxyapatite were evaluated by extended X-ray absorption fine structure measurements. The results indicated that there are specific sorption sites in Ca-deficient hydroxyapatite where Sr2+ is stably and preferentially immobilized.