An OFDM/offset QAM (OQAM)-IOTA system uses the isotropic orthogonal transform algorithm (IOTA) function, which has good localization properties in the time and frequency domains. This is employed instead of the guard interval used in a conventional OFDM/QAM system in order to be robust for multi-path channels. However, the conventional channel estimation scheme is not valid for an OFDM/OQAM-IOTA system due to the intrinsic inter-symbol interference of the IOTA function. In this paper, a condition is derived to reduce the intrinsic interference of the IOTA function. This condition is obtained with the proposed pilot structure used for perfect channel estimation. We also derive the preamble structure appropriate for practical channel estimation of the OFDM/OQAM-IOTA system. Simulation results show that the OFDM/OQAM-IOTA system with the proposed preamble structure performs better than the conventional OFDM system, and it has the additional advantage of an increased data transmission rate which corresponds to the guard interval retrieval.