A custom made implant is critical in cranioplasty to cushion and restore intracranial anatomy, as well as to recover the appearance and attain cognitive stability in the patient. The utilization of customized titanium alloy implants using three-dimensional (3D) reconstruction technique and fabricated using Electron Beam Melting (EBM) has gained significant recognition in recent years, owing to their convenience and effectiveness. Besides, the conventional technique or the extant practice of transforming the standard plates is unreliable, arduous and tedious. As a result, this work aims to produce a customized cranial implant using 3D reconstruction that is reliable in terms of fitting accuracy, appearance, mechanical strength, and consistent material composition. A well-defined methodology initiating from EBM fabrication to final validation has been outlined in this work. The custom design of the implant was carried out by mirror reconstruction of the skull’s defective region, acquired through computer tomography. The design of the customized implant was then analyzed for mechanical stresses by applying finite element analysis. Consequently, the 3D model of the implant was fabricated from Ti6Al4V ELI powder with a thickness of ≃1.76–2 mm. Different tests were employed to evaluate the bio-mechanical stability and strength of the fabricated customized implant design. A 3D comparison study was performed to ensure there was anatomical accuracy, as well as to maintain gratifying aesthetics. The bio-mechanical analysis results revealed that the maximum Von Mises stress (2.5 MPa), strain distribution (1.49 × 10−4) and deformation (3.26 × 10−6 mm) were significantly low in magnitude, thus proving the implant load resistance ability. The average yield and tensile strengths for the fabricated Ti6Al4V ELI EBM specimen were found to be 825 MPa and 880 MPa, respectively, which were well over the prescribed strength for Ti6Al4V ELI implant material. The hardness study also resulted in an acceptable outcome within the acceptable range of 30–35 HRC. Certainly, the chemical composition of the fabricated EBM specimen was intact as established in EDX analysis. The weight of the cranial implant (128 grams) was also in agreement with substituted defected bone portion, ruling out any stress shielding effect. With the proposed approach, the anatomy of the cranium deformities can be retrieved effectively and efficiently. The implementation of 3D reconstruction techniques can conveniently reduce tedious alterations in the implant design and subsequent errors. It can be a valuable and reliable approach to enhance implant fitting, stability, and strength.