Yes, joint pain can be caused by vitamin D deficiency. Prolonged vitamin C deficiency can also soften bones and cause limited joint pain. Vitamin D helps regulate the amount of calcium you absorb and excrete through your urine. If you are not either making (via exposure to sunlight) or consuming enough vitamin D in your diet (in fortified foods like cereals and milk), then your body may not keep calcium as well as it normally would and you may have weakened bones and joint pain.