Osteomalacia is a systemic metabolic bone disease. Hypophosphatemia is one of the most important causes of impaired mineralization. Here, we describe a case of osteomalacia associated with atypical renal tubular acidosis. A 43-year-old woman was admitted to our hospital due to sustained unrelieved bilateral flank pain. She had a history of fragile fracture with vitamin D deficiency and had been treated with active vitamin D. On admission, she presented with hypophosphatemia, hypocalcemia, high bone-specific alkaline phosphatase level, bone pain, and low bone mineral density. Multiple areas of uptake were also confirmed by bone scintigraphy, and she was diagnosed with osteomalacia. An increased dose of alfacalcidol was initiated for her vitamin D deficiency; her symptoms remained unstable and unrelieved. Her blood gas examination revealed metabolic acidosis without an increase in the anion gap (HCO3- 11.8 mEq/L, anion gap 3.2 mEq/L). Tubular dysfunction, tubular damage, kidney stones, and inadequate urinary acidification were all observed, suggesting the presence of renal tubular acidosis from a combination of both distal and proximal origin. She also had overt proteinuria, decreased renal function, and hypothalamic hypogonadism. In addition to alfacalcidol, sodium bicarbonate and oral phosphorus supplementation were initiated. After this prescription, her pain dramatically improved in association with the restoration of acid-base balance and electrolytes; renal dysfunction and proteinuria were unaltered. This case indicated that careful assessments of tubular function and acid-base balance are essential for the management of osteomalacia in addition to the evaluation of the calcium/phosphate balance and vitamin D status.