Ultra low-loss microwave materials are crucial for enhancing quantum coherence and scalability of superconducting qubits. Van der Waals (vdW) heterostructure is an attractive platform for quantum devices due to the single-crystal structure of the constituent two-dimensional (2D) layered materials and the lack of dangling bonds at their atomically sharp interfaces. However, new fabrication and characterization techniques are required to determine whether these structures can achieve low loss in the microwave regime. Here we report the fabrication of superconducting microwave resonators using NbSe$_2$ that achieve a quality factor $Q > 10^5$. This value sets an upper bound that corresponds to a resistance of $leq 192 muOmega$ when considering the additional loss introduced by integrating NbSe$_2$ into a standard transmon circuit. This work demonstrates the compatibility of 2D layered materials with high-quality microwave quantum devices.