4G/5G wireless standards use orthogonal frequency division multiplexing (OFDM) which is robust to frequency selectivity. Equalization is possible with a single tap filter, and low-complexity equalization makes OFDM an attractive physical layer. However the performance of OFDM degrades with mobility, since Doppler spreads introduce inter-carrier interference (ICI) between subcarriers and they are no longer orthogonal. Zak-transform based orthogonal time frequency space (Zak-OTFS) modulation has been shown to be robust to doubly selective channels. Zak-OTFS signals are formed in the delay-Doppler (DD) domain, converted to time domain (TD) for transmission and reception, then returned to the DD domain for processing. The received signal is a superposition of many attenuated copies since the doubly selective channel introduces delay and Doppler shifts. The received symbols are more difficult to equalize since they are subject to interference along both delay and Doppler axes. In this paper, we propose a new low-complexity method of equalizing Zak-OTFS in the frequency domain (FD). We derive the FD system model and show that it is unitarily equivalent to the DD system model. We show that the channel matrix in the FD is banded, making it possible to apply conjugate gradient methods to reduce the complexity of equalization. We show that complexity of FD equalization is linear in the dimension of a Zak-OTFS frame. For comparison the complexity of naive MMSE equalization is cubic in the frame dimension. Through numerical simulations we show that FD equalization of Zak-OTFS achieves similar performance as equalization in DD domain.