The 41-year-old children's doctor had admitted to all the cases - including aggravated sexual abuse, rape and false imprisonment -- in his trial in the southern city of Augsburg.
He was also barred for life from the medical profession after admitting to his 15-year series of sexual assaults, reported public broadcaster Bayerischer Rundfunk and national news agency DPA.
The unidentified man had worked at Augsburg Hospital, the Medical University of Hannover and the German Heart Centre in Munich. He had also been a board member of the Bavarian Red Cross.
He had abused his position of trust as a doctor and used drugs from his emergency medical case to sedate his victims, then filmed and photographed the boys while abusing them.
In August 2014, he lured a five-year-old into his car, sedated him and assaulted him in his apartment before releasing him back at the spot where he abducted him, in Garbsen, Lower Saxony state.
Police caught the man through DNA and cellphone data, which connected several crimes of the paediatrician, who had also lured children into basement areas in the cities of Augsburg and Munich.
He was sentenced to 13 and a half years jail to be followed by preventive detention, one year short of the jail term prosecutors had demanded.
The defence lawyer had asked for nine years jail to be followed by treatment in a psychiatric hospital.
A search of the man's home recovered more than 50,000 electronic files of child pornography, the court heard.
The court ordered that after serving his term he would remain in preventive detention, which aims to protect the public from offenders as long as they are still considered dangerous.