Background: Adequate calcium intake at an early age is crucial to achieving peak bone mass. Nevertheless, low calcium intake is common in Malaysian children. Aim: This study examined the calcium food sources and factors associated with low calcium intake among 243 children aged 9–11 years in Kuala Lumpur. Methods: Diet histories and bone density were measured. Results: The mean calcium intake was 370 ± 187 mg/day. The main contributors to calcium intake were beverages (19.2%), cereal (18.6%), milk and dairy (13.0%), meat and poultry (12.9%), and fish and seafood (10.1%). Within each food group, calcium-contributing foods tend to be from low bioavailability sources such as rice, cocoa-based and malted drinks, and chicken rather than milk. Children who practised regular meals, ate breakfast and snacks and consumed milk more than one serving daily have a higher calcium intake. Conclusion: In conclusion, public health strategies to improve the status of low calcium intake and poor choices of calcium-rich foods are needed to optimise bone health in this population.