In order to realize fault-tolerant quantum computation, a tight evaluation of the error threshold under practical noise models is essential. While non-Clifford noise is ubiquitous in experiments, the error threshold under non-Clifford noise cannot be efficiently treated with known approaches. We construct an efficient scheme for estimating the error threshold of the one-dimensional quantum repetition code under non-Clifford noise. To this end, we employ the nonunitary free-fermionic formalism for efficient simulation of the one-dimensional repetition code under coherent noise. This allows us to evaluate the effect of coherence in noise on the error threshold without any approximation. The result shows that the error threshold becomes one-third when the noise is fully coherent. Our scheme is also applicable to the surface code undergoing a specific coherent noise model. The dependence of the error threshold on noise coherence can be explained with a leading-order analysis with respect to coherence terms in the noise map. We expect that this analysis is also valid for the surface code since it is a two-dimensional extension of the one-dimensional repetition code. Moreover, since the obtained threshold is accurate, our results can be used as a benchmark for the approximation or heuristic schemes for non-Clifford noise.