Perlecan, a heparan sulfate proteoglycan, acts as a mechanical sensor for bone to detect external loading. Deficiency of perlecan increases the risk of osteoporosis in patients with Schwartz-Jampel Syndrome (SJS) and attenuates loading-induced bone formation in perlecan deficient mice (Hypo). Considering that intracellular calcium [Ca²⁺+]i is an ubiquitous messenger controlling numerous cellular processes including mechanotransduction, we hypothesized that perlecan deficiency impairs bone’s calcium signaling in response to loading. To test this, we performed real-time [Ca²⁺+]i imaging on in situ osteocytes of adult murine tibiae under cyclic loading (8 N). Relative to wild type (WT), Hypo osteocytes showed decreases in the overall [Ca²⁺+]i response rate (−58%), calcium peaks (−33%), cells with multiple peaks (−53%), peak magnitude (−6.8%), and recovery speed to baseline (−23%). RNA sequencing and pathway analysis of tibiae from mice subjected to one or seven days of unilateral loading demonstrated that perlecan deficiency significantly suppressed the calcium signaling, ECM-receptor interaction, and focal adhesion pathways following repetitive loading. Defects in the endoplasmic reticulum (ER) calcium cycling regulators such as Ryr1/ryanodine receptors and Atp2a1/Serca1 calcium pumps were identified in Hypo bones. Taken together, impaired calcium signaling may contribute to bone’s reduced anabolic response to loading, underlying the osteoporosis risk for the SJS patients.