Recently, single carrier block transmission with frequency domain equalization (SC-FDE) has been shown to be a promising candidate for ultra-wideband (UWB) communications. In this paper, we address the channel estimation problem for SC-FDE transmission over UWB channels. A mean square error (MSE) lower bound for the frequency domain LMMSE channel estimator is derived and the optimal pilot sequence that achieves this lower bound is obtained. Further simplification leads to a frequency domain channel estimator with reduced computational complexity. The performance of the simplified estimator for SC-FDE over UWB channels is evaluated and compared with that of perfect channel state information. The effects of non-optimal and optimal pilot symbols are also investigated. Our results show that the proposed frequency domain channel estimator performs well over UWB channels with only small performance degradation compared to the perfect channel estimation