Phelan-McDermid syndrome (PHMDS)/22q13.3 deletion syndrome is a rare genetic disorder associated with autism spectrum disorder (ASD), intellectual disability (ID), and bipolar disorder. While numerous cases have been reported describing successful pharmacological treatment of bipolar disorder in PHMDS, there is currently little guidance available on how to organize and execute such treatment. The aim of the current case study was to explore how pharmacological treatment of bipolar disorder in PHMDS may be organized and evaluated in an outpatient setting. Through a complex process of try and fail, including systematic evaluation of any change to the intervention and never implementing more than one change at the time, the patient gradually improved, regaining his communicative and adaptive skills. Four years passed from referral to this result was achieved. Organizing assessment and treatment as a collaborative effort involving specialized mental health professionals, professional caregivers and the patient's family proved feasible. Many of the challenges present in assessment of psychiatric disorder in individuals with ASD and ID are likely to be present also in evaluation of treatment effects, particularly in disorders where symptoms occur in phases. The approach described in the current paper may contribute to reducing the impact of these challenges.