Objectives Research into meditation-related emergent phenomenology is advancing, yet progress is hampered by significant incongruities between meditator self-reports and objective measurements (e.g., of brain states). We address these incongruities by developing and demonstrating the potential of contemplative theory to support scientific investigation. Method Our approach is to translate key theories from Buddhist contemplative traditions into scientific terms, and then systematize these translations as a functionalist model of the mind—the Thin Model—able to inform scientific inquiry. Results Buddhist doctrine is shown to be consistent with objective descriptions of mental function, and the Thin Model derived from these translations demonstrates immediate explanatory power. The nested nature of the model allows explanations to be restricted to the specific problem being studied. The model enables connection of complex higher-level phenomena, such as self-reports of mental states, to complex lower-level phenomena, such as empirically measured brain states. This connection does not require simplistic assumptions to be made. A detailed demonstration illustrates how the model can convert subjective accounts of the ecstatic meditative states known as jhānas into testable neuroscientific hypotheses. Conclusions We provide an account of contemplative theory that is amenable to scientific investigation. Our approach, exemplified in the Thin Model, offers immediate explanatory power, allows meaningful dialogue between different research traditions, and provides an organizing principle for explanations of mental phenomena. The Thin Model may also be relevant to other fields concerned with autonomous entities or the nature and operation of the mind.