Hydroxyapatite (HA) and HA-based nanocomposites have been recognized as ideal biomaterials in hard tissue engineering because of their compositional similarity to bioapatite. However, the traditional HA-based nanocomposites fabrication techniques still limit the utilization of HA in bone, cartilage, dental, applications, and other fields. In recent years, three-dimensional (3D) printing has been shown to provide a fast, precise, controllable, and scalable fabrication approach for the synthesis of HA-based scaffolds. This review therefore explores available 3D printing technologies for the preparation of porous HA-based nanocomposites. In the present review, different 3D printed HA-based scaffolds composited with natural polymers and/or synthetic polymers are discussed. Furthermore, the desired properties of HA-based composites via 3D printing such as porosity, mechanical properties, biodegradability, and antibacterial properties are extensively explored. Lastly, the applications and the next generation of HA-based nanocomposites for tissue engineering are discussed.