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We study the secret key rate (SKR) of a multiple-input multiple-output (MIMO) continuous variable quantum key distribution (CVQKD) system operating at terahertz (THz) frequencies, accounting for the effects of channel estimation. We propose a practical channel estimation scheme for the THz MIMO CVQKD system which is necessary to realize transmit-receive beamforming between Alice and Bob. We characterize the input-output relation between Alice and Bob during the key generation phase, by incorporating the effects of additional noise terms arising due to the channel estimation error and detector noise. Furthermore, we analyze the SKR of the system and study the effect of channel estimation error and overhead. Our simulation results reveal that the SKR may degrade significantly as compared to the SKR upper bound that assumes perfect channel state information, particularly at large transmission distances.