Midazolam is a positive allosteric modulator at GABAA receptor that induces a short hypnosis and neuroplasticity, in which the sequential phosphorylation of MEK1/2 and ERK1/2 was shown to play a role. This study investigated the parallel activation of p-MEK and p-ERK and regulatory mechanisms induced by midazolam through the stimulation of GABAA receptors in the mouse brain. During the time course of midazolam (60 mg/kg)-induced sleep in mice (lasting for about 2 h) p-Ser217/221 MEK1/2 was increased (+ 146% to + 258%) whereas, unexpectedly, p-Tyr204/Thr202 ERK1/2 was found decreased (− 16% to − 38%), revealing uncoupling of MEK to ERK signals in various brain regions. Midazolam-induced p-MEK1/2 upregulation was prevented by pretreatment (30 min) with flumazenil (10 mg/kg), indicating the involvement of GABAA receptors. Also unexpectedly, midazolam-induced p-ERK1/2 downregulation was not prevented by flumazenil (10 or 30 mg/kg). Notably, during midazolam-induced sleep the content of inactivated p-Thr286 MEK1, which can dampen ERK1/2 activation, was increased (+ 33% to + 149%) through a mechanism sensitive to flumazenil (10 mg/kg). Midazolam also increased MKP-3 (+ 13% to + 73%) content and this upregulation was prevented by flumazenil (10 mg/kg); an effect suggesting ERK inactivation because MKP-3 is the phosphatase selective for ERK1/2 dephosphorylation. The results indicate that during midazolam-induced sleep in mice there is an uncoupling of p-MEK (increased) to p-ERK (decreased) signals. p-ERK1/2 downregulation (not involving GABAA receptors) is the result of increased inactivated MEK1 and phosphatase MKP-3 (both effects involving GABAA receptors). These findings are relevant for the neurobiology and clinical use of benzodiazepines.