Introduction We propose a model of the interactions between the nervous systems and the rest of the body which explains why and how mindfulness training is beneficial in stress management and for stress related psychological and physical problems. The hypothesis behind the model is that a major component of chronic stress is due to mind-wandering and rumination, which tend to continuously activate the sympathetic nervous system and the stress response. The focus on the present moment decreases mind-wandering (Brewer et al. 2011, Mrazek et al. 2013), which in turn allows to deactivate the sympathetic system and activate the parasympatethic system (Tang et al. 2009), decreasing stress and improving physical and mental well-being. Method Our model includes a set of simulated areas strongly related to mindfulness and mind-wandering, including different parts of the prefrontal cortex, the amygdala, the hypothalamus, as well as a simulation of the sympathetic and parasympathetic systems. Results The model explains the mechanisms behind the effects of mindfulness on stress reduction on the basis of the reciprocal interactions between the body and several neural systems, and the sympathetic and parasympathetic branches of the autonomous nervous system. Discussion We show how the model can be implemented in a working neurocomputationl model which may reproduce and explain different kinds of empirical phenomena related to mindfulness training, both neural (e.g. increase in prefrontal cortex and decrease in amygdala activations: Taylor et al. 2011, Holzel et al. 2013), and physiological (e.g. increase in parasympathetic and decrease in sympatetic activities: Rubia 2009).