At Kyoto University Research Reactor Institute, clinical studies of around 400 of Boron Neutron Capture Therapy (BNCT) have been performed using research reactor. On the other hand, we have developed cyclotron based epithermal neutron source. To improve the quality of treatment, it is necessary to perform the detection of two dimensional thermal neutron distribution before and during treatment as quality control. Generally, the method of activation using gold foil/wire and germanium semiconductor detector is applied to detection of thermal neutron flux at several positions. However, the activation method using semiconductor detector takes some time to decide the thermal neutron flux. Therefore, we propose the method using multi-wire proportional counter for detection of two dimensional thermal neutron distribution. We constructed the system consisting of multi-wire detection head, multi-channel preamplifier, multi-channel discriminator, centroid calculation circuit, and data acquisition system. Detection efficiency for BNCT irradiation field was evaluated using Am-Be neutron source with moderator for producing thermal neutrons. Furthermore, two dimensional thermal neutron distribution was demonstrably obtained.