Regeneration of lost tissues depends on the precise interpretation of molecular signals that control and coordinate the onset of proliferation, cellular differentiation and cell death. However, the nature of those molecular signals and the mechanisms that integrate the cellular responses remain largely unknown. The planarian flatworm is a unique model in which regeneration and tissue renewal can be comprehensively studied in vivo. The presence of a population of adult pluripotent stem cells combined with the ability to decode signaling after wounding enable planarians to regenerate a complete, correctly proportioned animal within a few days after any kind of amputation, and to adapt their size to nutritional changes without compromising functionality. Here, we demonstrate that the stress-activated c-jun–NH2–kinase (JNK) links wound-induced apoptosis to the stem cell response during planarian regeneration. We show that JNK modulates the expression of wound-related genes, triggers apoptosis and attenuates the onset of mitosis in stem cells specifically after tissue loss. Furthermore, in pre-existing body regions, JNK activity is required to establish a positive balance between cell death and stem cell proliferation to enable tissue renewal, remodeling and the maintenance of proportionality. During homeostatic degrowth, JNK RNAi blocks apoptosis, resulting in impaired organ remodeling and rescaling. Our findings indicate that JNK-dependent apoptotic cell death is crucial to coordinate tissue renewal and remodeling required to regenerate and to maintain a correctly proportioned animal. Hence, JNK might act as a hub, translating wound signals into apoptotic cell death, controlled stem cell proliferation and differentiation, all of which are required to coordinate regeneration and tissue renewal. Planarians, thanks to their extraordinary regenerative capacity, represent a unique model of animal regeneration. After amputation, new animals regenerate from each individual piece of tissue, leading Dalyell to describe them as “immortal under the edge of the knife” in 1814. Planarians also continuously renew their tissues and adapt their size in accordance with nutritional supply. This amazing plasticity relies on the presence of a population of adult pluripotent stem cell, the neoblasts. However, little is known about the mechanisms that trigger cell responses, such as cell death and division, which are required to regenerate and maintain tissues and organs in response to injury or nutritional challenge. Here, we show that JNK acts as a hub in the coordination of these events. Specifically in response to tissue loss, JNK modulates the expression of wound-related genes, induces the elimination of unnecessary cells by apoptotic cell death and controls cell division in neoblasts. Loss of JNK function results in the deregulation of these processes and prevents regeneration. Moreover, we demonstrate that JNK-dependent apoptosis is crucial to generate proportioned organisms during tissue turnover. Our findings reveal a central mechanism in planarians that senses tissue loss and translates this information into cellular responses leading to regeneration and tissue renewal.