•  Previously demonstrated facilitation of activation of subcortical neurons by transcranial direct current stimulation (tDCS) in acute experiments on deeply anaesthetized animals was fairly weak. It resulted in only small increases in the amplitude and in a slight shortening of latencies of subcortically initiated descending volleys. •  Here we show that despite weak effects on descending volleys, EMG responses evoked in neck muscles by reticulospinal and rubrospinal neurons in deeply anaesthetized non‐paralysed rats are potently facilitated by tDCS and that the facilitation outlasts tDCS. •  We further show that the facilitatory subcortical effects of tDCS in the rat are evoked by cathodal rather than anodal polarization, i.e. by a polarity that is the reverse of that most often found to be effective in humans and in the cat. Anodal polarization depressed activation of the same rat subcortical neurons. •  These findings should assist further studies of mechanisms of tDCS in vivo in rodents. Abstract  Transcranial direct current stimulation (tDCS) affects neurons at both cortical and subcortical levels. The subcortical effects involve several descending motor systems but appeared to be relatively weak, as only small increases in the amplitude of subcortically initiated descending volleys and a minute shortening of latencies of these volleys were found. The aim of the present study was therefore to evaluate the consequences of facilitation of these volleys on the ensuing muscle activation. The experiments were carried out on deeply anaesthetized rats without neuromuscular blockade. Effects of tDCS were tested on EMG potentials recorded from neck muscles evoked by weak (20–60 μA) single, double or triple stimuli applied in the medial longitudinal fascicle (MLF) or in the red nucleus (RN). Short latencies of these potentials were compatible with monosynaptic or disynaptic actions of reticulospinal and disynaptic or trisynaptic actions of rubrospinal neurons on neck motoneurons. Despite only weak effects on indirect descending volleys, the EMG responses from both the MLF and the RN were potently facilitated by cathodal tDCS and depressed by anodal tDCS. Both the facilitation and the depression developed relatively rapidly (within the first minute) but both outlasted tDCS and were present for up to 1 h after tDCS. The study thus demonstrates long‐lasting effects of tDCS on subcortical neurons in the rat, albeit evoked by an opposite polarity of tDCS to that found to be effective on subcortical neurons in the cat investigated in the preceding study, or for cortical neurons in the humans.