Background Due to the civil war in Syria, many Syrian citizens have had to flee their country during recent years, among them many physicians. Germany is among the preferred immigration countries. Immigrant Syrian physicians could help overcome the prevailing shortage of medical specialists in Germany. This study explores the experiences and perceptions of Syrian physicians of the licensure process and job application. The study aims at understanding barriers in integrating Syrian doctors into the German health care system. Methods We conducted 20 semi standardized interviews with Syrian doctors (n = 17 m; n = 3 f) living in different federal states in Germany. The interviews dealt with the procedure of the accreditation process, its speed and challenges, the interactions with authorities, and the job application process; they were transcribed verbatim. A detailed content analysis was performed. Results All interviewees described the licensure process as a complex, lengthy, ever-changing and non-transparent procedure, which is perceived as a partly unfair, sometimes arbitrary bureaucracy. They often feel at mercy of Government employees and report experiences with reviewers who ask for absurd and impossible accomplishments, refuse to give information, and act at random. As a consequence, the interviewees describe themselves as depressed, irritated and/or in despair. According to the interviews, informational and practical support from official institutions was scarce. Instead, the Syrian doctors relied on peers or, in some cases, German friends to understand the requirements and seek information about the licensure process. To find a job placement, it was very helpful, if not essential, to have a German acquaintance establishing contact with possible employers. All three interviewed female doctors reported that their wearing a Hijab led to episodes of discrimination in their job search. Conclusions The study points towards the necessity to establish an official information source which provides immigrant doctors with accurate and detailed information about the licensure process, e.g. required documents, estimated waiting times, regulation for courses and exams, criteria regarding credentials, sources of help, etc. Additionally, it seems advisable to consider providing help with regard to the job search and sensitize hospital management for cultural and religious diversity to avoid discrimination.