For increasing the output of biofuel cells, increasing the cooperation between enzyme reaction and electron transfer on the electrode surface is essential. Highly oriented immobilization of enzymes onto a carbon nanotube (CNT) with a large specific surface area and excellent conductivity would increase the potential for their application as biosensors and biofuel cells, by utilizing the electron transfer between the electrode-molecular layer. In this study, we prepared a CNT-enzyme complex with highly oriented immobilization of enzyme onto the CNT surface. The complex showed excellent electrical characteristics, and could be used to develop biodevices that enable efficient electron transfer. Multi-walled carbon nanotubes (MWCNT) were dispersed by pyrene butyric acid N-hydroxysuccinimide ester, and then N-(5-amino-1-carboxypentyl) iminodiacetic acid (AB-NTA) and NiCl₂ were added to modify the NTA-Ni2+ complex on the CNT surface. Pyrroloquinoline quinone (PQQ)-dependent glucose dehydrogenase (GDH) was immobilized on the CNT surface through a genetically introduced His-tag. Formation of the MWCNT-enzyme complex was confirmed by monitoring the catalytic current electrochemically to indicate the enzymatic activity. PQQ-GDH was also immobilized onto a highly ordered pyrolytic graphite surface using a similar process, and the enzyme monolayer was visualized by atomic force microscopy to confirm its structural properties. A biofuel cell was constructed using the prepared CNT-enzyme complex and output evaluation was carried out. As a result, an output of 32 μW/cm² could be obtained without mediators.