This paper presents a novel evaluation method for designing an intuitive surgical robot by measuring a user's brain activity. Conventionally, surgical robots have been designed based on their mechanical performance. However, an improvement in a robot's mechanical performance does not necessarily represent the embodiment that the user feels. In this paper, we evaluate intuitive operability based on the user's brain activation. Previously, we used functional near-infrared spectroscopic-topography (fNIRS) brain imaging; however, it is better to use a brain measurement technique possessing a high time resolution, as brain activity is has a higher time resolution than fNIRS. The objective was to measure changes in brain activity as a function of a change in the slave arm positioning. In the experiment, the brain activity of four participants was measured using fNIRS while they used a hand controller to move the virtual arm of a surgical simulator. The experiment was carried out with the virtual arm in two positions: one easy to control and the other difficult. The spectrum of the brain activity increased at the easy position more than at the difficult position. We conclude that the brain activity changed as the user perceived that the virtual arm belonged to their body.