Bone, an intricately interconnected and constantly evolving tissue in the human body, continuously undergoes modeling and remodeling processes to maintain the structural integrity of the skeletal system. The repair of small bone defects is generally attributed to spontaneous self-healing and remodeling processes. However, bone’s self-repair capacity often proves inadequate when confronted with extensive bony defects, known as “critical-sized defects.” Consequently, the use of bone grafts has become crucial for enhancing or promoting new bone formation in these extensive defect sites. A range of alternatives to bone grafts are presently utilized to promote the regeneration of bone tissue. Polyhydroxyalkanoates (PHAs), a highly encouraging group of aliphatic polyesters produced by various microorganisms, show great potential. Their natural origin, biocompatibility, and biodegradability, coupled with their diverse mechanical and physicochemical properties, make PHAs highly suitable for medical device applications. This article presents a thorough examination of the characteristics of PHAs, their utilization in bone tissue engineering, and the application of innovative manufacturing methods to create scaffolds based on PHAs. It also discusses the challenges associated with PHA application, including high production costs, mechanical adaptability, and degradation issues. Finally, it presents an outlook on future research priorities.