Neural interface in the form of microelectrodes is used to monitor and treat spinal cord injury and other neurological disorders by the means of recording and stimulation. Despite the apparent result of these electrical interventions, understanding of the mechanism behind neural stimulation is still inadequate. The use of optical monitoring during implantation is limited due to the use of opaque electrode partially blocking the implantation site. While the use of transparent conductor for an electrode is not uncommon in general electronics where indium tin oxide (ITO) is widely used for displays, however ITO is not suitable for implantation due to its brittle nature[1]. An alternative material to fabricate transparent electrodes is graphene, a single layer of carbon atom forming sp2 hybridization. Its high charge mobility, flexibility, mechanical strength, and optical transparency make it suitable for various flexible electronics applications including implantable microelectrode arrays. In biomedical fields, graphene has shown potential application as biosensor, stimulation and recording electrode[2]. Although fabrication of graphene microelectrodes has been previously shown[3], graphene had to be transferred manually for each layer. The high temperature needed during graphene deposition makes device fabrication directly on the flexible material impossible. Instead, the fabrication process relies on a transferring process of graphene layer from a growing medium with a high thermal budget to another desired substrate. The manual transfer process of graphene is a skill-dependant process with low scalability. In this work, a method of fabricating encapsulated graphene electrodes in polydimethylsiloxane (PDMS) with a controlled wafer-scale graphene transfer is proposed. Graphene transfer is done by wafer-assisted PDMS-PDMS bonding. The novel use of PDMS as an encapsulation material for graphene electrode is due to its biocompatibility, flexibility and optical transmittance. The transferred graphene was patterned on the PDMS by using oxygen plasma. Holes with a diameter of 10 μm was able to be patterned while maintaining the conductivity of the graphene layer. A combination of titanium and aluminium was used as metal contacts, the titanium provides a good contact resistance to graphene layer while aluminium allows wire bonding process to be performed on the contacts. Difference in material characteristics, such as the thermal expansion coefficient has become one of the challenges during the fabrication process. Despite these challenges, the fabrication process for the electrode array was designed and tested. Conductivity of the patterned graphene layer was tested. The optical transmittance measurement showed up to 77% transmittance was achieved on the graphene encapsulated by PDMS.