Hyperekplexia disease is usually caused by naturally occurring point mutations in glycine receptors (GlyRs). However, the γ-aminobutyric acid type A receptor (GABAR) seems to be also involved regarding the therapeutic basis for hyperekplexia using benzodiazepines, which target GABARs but not GlyRs. Here, we show that the function of GABARs was significantly impaired in the hypoglossal nucleus of hyperekplexic transgenic mice. Such impairment appeared to be mediated by interaction between GABAR and mutant GlyR. The GABAR dysfunction was caused only by mutant GlyR consisting of homomeric α subunits, which locate primarily at pre- and extra-synaptic sites. In addition, the rescue effects of diazepam were attenuated by Xli-093, which specifically blocked diazepam-induced potentiation on α-containing GABAR, a major form of pre- and extra-synaptic GABAR in the brainstem. Thus, our results suggest that the pre- and extra-synaptic GABARs could be a potential therapeutic target for hyperekplexia disease caused by GlyR mutations.