The locus coeruleus (LC) projects throughout the brain and spinal cord and is the major source of central noradrenaline. It remains unclear whether the LC acts functionally as a single global effector or as discrete modules. Specifically, while spinal-projections from LC neurons can exert analgesic actions, it is not known whether they can act independently of ascending LC projections. Using viral vectors taken up at axon terminals, we expressed chemogenetic actuators selectively in LC neurons with spinal (LC^:SC) or prefrontal cortex (LC^:PFC) projections. Activation of the LC^:SC module produced robust, lateralised anti-nociception while activation of LC^:PFC produced aversion. In a neuropathic pain model, LC^:SC activation reduced hind-limb sensitisation and induced conditioned place preference. By contrast, activation of LC^:PFC exacerbated spontaneous pain, produced aversion and increased anxiety-like behaviour. This independent, contrasting modulation of pain-related behaviours mediated by distinct noradrenergic neuronal populations provides evidence for a modular functional organisation of the LC.