The Schöneberg court ruling came after the man's year-long court battle to be named father, Bild newspaper reported.
The 31-year-old had undergone a sex change via hormone treatment, but retained female sexual organs and went on to become pregnant a year after legally becoming a man.
The judge defended the ruling as a simple matter of course. "Every child has a mother, and that is the person who gave birth to them. Your name will be recorded on that basis," he said.
The judge's summary went on to say the fact the "mother" was legally a man played no role in the decision, Bild said.
After the child's birth last March, the father asked to be listed as such on the birth certificate, claiming that even though he gave birth to the baby, he was a man and therefore could not be its mother.
But the question of whether the man, who became pregnant by a sperm donation, should be listed as father and sole parent, sparked public debate and has been under discussion in the Schöneberg court since last April.
CDU Neukölln district councillor Falko Lieke fiercely supported the court's decision to keep "mother" on the birth register, despite earlier speaking out in defence of the transsexual's right to parenthood.
"It ensures that at some point, the child will find out who their real mother is," he said. "It is egotistical to keep your own child in the dark while you prioritize your own gender identity."
But some observers might be less satisfied by the result.
Biology and sex researcher Heinz-Jürgen Voß told Berliner Morgenpost newspaper in September the gender of the registered parent should not be considered so important.
"A transgender person having children is not problematic. Why is the sex asked on every form? The problem is this classification. Why isn't the name enough?"
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