Despite predictions that neuroscientific discoveries would revolutionize psychiatry, decades of research have not yet led to clinically significant advances in psychiatric care. For this reason, an increasing number of researchers are recognizing the limitations of a purely biomedical approach in psychiatric research. These researchers call for reevaluating the conceptualization of mental disorders and argue for a non‐reductionist approach to mental health. The aim of this paper is to discuss philosophical assumptions that underly neuroscientific research in psychiatry and offer practical tools to researchers for overcoming potential conceptual problems that are derived from those assumptions. Specifically, we will discuss: the analogy problem, questioning whether mental health problems are equivalent to brain disorders, the normativity problem, addressing the value‐laden nature of psychiatric categories and the priority problem, which describes the level of analysis (e.g., biological, psychological, social, etc.) that should be prioritized when studying psychiatric conditions. In addition, we will explore potential strategies to mitigate practical problems that might arise due to these implicit assumptions. Overall, the aim of this paper is to suggest philosophical tools of practical use for neuroscientists, demonstrating the benefits of a closer collaboration between neuroscience and philosophy.