Background This study aims to evaluate the accuracy of volumetric measurements of three-dimensional (3D)-printed human condyles from cone-beam computed tomography (CBCT) in comparison to physical condyles using a water displacement test. Methodology A sample of 22 dry condyles was separated from the mandibular body by disc, mounted on a base made of casting wax, and scanned using the SCANORA (Scanora 3DX, Soredex, Finland) CBCT scanner. Subsequently, the projection data were reconstructed with the machine-dedicated OnDemand 3D (Cybermed Co., Seoul, Korea). The Standard Tessellation Language file was prepared for 3D printing using chitubox slicing software v1.9.1. Frozen water-washable gray resin was used for 3D printing. All condyles were printed using the same parameters and the same resin. The volumetric measurements were then performed using a customized modified pycnometer based on water volume and weight displacement. Volumetric measures were performed for both the physical human condyles and the 3D-printed replicas and the measurements were then compared. Results The volume of dry condyles using the water displacement method showed an average (±SD) of 1.925 ± 0.40 cm3. However, the volume of 3D-printed replicas using the water displacement method showed an average (±SD) of 2.109 ± 0.40 cm3. The differences in measurements were insignificant (p > 0.05), as revealed by an independent t-test. Conclusions Highly precise, accurate, and reliable CBCT for volumetric mandibular condyle was applied for measurements of a human condyle and 3D-printed replica. The modified pycnometer for volumetric measurements presented an excellent volumetric measure based on a simple water displacement device. The tested modified pycnometer can be applied in volumetric measurements in both 3D-printed and mandibular condyle. For best accuracy, the highest scanning resolution possible should be used. As it directly handles irregularly shaped solid objects in a non-destructive manner with a high level of precision and reliability, this 3D scanning approach may be seen as a superior alternative to the current measurement methods.