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The present paper focuses the application of the base station cooperation (BSC) technique in fractional frequency reuse (FFR) networks. Fractional frequency reuse is considered to be a promising scheme for avoiding the inter-cell interference problem in OFDMA cellular systems, such as WiMAX, in which the edge mobile stations (MSs) of adjacent cells use different subchannels for separate transmission. However, the problem of FFR is that the cell edge spectral efficiency (SE) is much lower compared to that of the cell center. The BSC technique, in which adjacent BSs perform cooperative transmission for one cell edge MS with the same channel, may improve the cell edge SE. However, since more BSs transmit signals for one cell edge MS, the use of BSC can also increase the inter-cell interference, which might degrade the network performance. In the present paper, with a focus on this tradeoff, we propose an adaptive BSC scheme in which BSC is only performed for the cell edge MSs that can achieve a significant capacity increase with only a slight increase in inter-cell interference. Moreover, a channel reallocation scheme is proposed in order to further improve the performance of the adaptive BSC scheme. The simulation results reveal that, compared to the conventional FFR scheme, the proposed schemes are effective for improving the performance of FFR networks.