He is specialised in conducting randomised controlled trials and meta-analyses on prevention and psychological treatments of common mental disorders across the life span. Much of his work is aimed at prevention of mental disorders, psychological treatments of depression and anxiety disorders, and Internet-delivered treatments.

He has also published on several other research topics, including global mental health, student mental health, and psycho-oncology. Pim Cuijpers has published more than 1,200 peer-reviewed papers, chapters, reports and professional publications, including more than a 1,000 papers in international peer-reviewed scientific journals.