Recently, Gualtiero Piccinini and Carl Craver (2011) have argued that functional analyses in psychology lack explanatory autonomy from explanations in neuroscience. In this thesis I argue against this claim by motivating and defending a pragmatic-epistemic conception of autonomous psychological explanation. I argue that this conception of autonomy need not require that functional analyses be distinct in kind from neural-mechanistic explanations. I use the framework of Bas van Fraassen’s Pragmatic Theory of Explanation (van Fraassen 1980) to show that explanations in psychology and neuroscience can be seen as seeking understanding of autonomous levels of mechanistic phenomena.