This review aims to provide a guidance in the decision process when to choose a janus kinase (JAK) inhibitor as medical treatment strategy. The focus will be on ulcerative colitis, since the only yet available JAK inhibitor, tofacitinib, has the approval for ulcerative colitis. The guidance path will include consideration on disease activity, previous treatment, comorbidities, family planning, patients’ preferences, pharmacology as well as concurrent chronic inflammatory diseases or extraintestinal manifestations. The suggested guidance path illustrates our daily difficulties in the decision process of making the best choice for the individual patient. However, as long as predictive biomarkers are lacking, the named criteria can be applied to any other strategy and hence provide support in daily practice.