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The alignment of neuroscientific research with psychoanalytic theory and practice has led researchers in the emerging field of neuropsychoanalysis to scrutinize their metaphysical assumptions with respect to the relationship between mind and matter. The position which has achieved prevalence is dual-aspect monism. However, this trend is naïve to the fact that no consensus has been reached on the mind–body problem in the philosophy of mind literature. Moreover, like all metaphysical positions, dual-aspect monism contains conceptual flaws and is inconsistently defined, but these issues have not been sufficiently addressed in the neuropsychoanalytic literature. The present study reviews materialism, dual-aspect monism and transcendental idealism as candidate positions on which to ground neuropsychoanalytic thought. Whilst materialism holds that mind is ultimately reducible to material processes and dual-aspect monism holds that mind and matter are two irreducible perspectives on one underlying ontological domain, Kantian transcendental idealism views both mental and physical processes as subjective representations of a numinous reality which cannot be experienced directly. Instances are highlighted where neuropsychoanalytic dual-aspect monism slips into tacit forms of materialism and transcendental idealism. Transcendental idealism is conceived of as an epistemologically modest position which holds that inquiry into the mind–body relationship can only begin through exploring the boundaries of representation. It is submitted that the neuropsychoanalytic approach to the mind–body problem is implicitly aligned with transcendental idealism, and that this should be stated explicitly. Some clinical implications of these variations in metaphysical framing are discussed.