Orthogonal precoded (OP)-orthogonal frequency-division multiplexing (OFDM) is an OFDM scheme with invertible precoding. As previously reported, slight redundancy in data transmission orthogonal precoding to efficiently suppress high out-of-band emission (OOBE) of traditional OFDM signals. On the other hand, precoding generally affects modulating symbols on all subcarriers, and thus, prevents classical channel estimation schemes based on pilot subcarriers. This study investigates a design to protect the pilot subcarriers in the OP-OFDM system and proposes an efficient semi-blind channel estimation method to reuse the redundancy of the precoding. Numerical experiments are conducted in the context of satisfying a strict spectral mask of 50 dB at band-edges by the OP-OFDM system with the pilot subcarriers. The experimental results show that the proposed method can estimate channel responses over all the subcarriers at a high accuracy equivalent to the counterpart on the pilot subcarriers.