He was named after his father's brother, who was a clergyman and a poet. When Fibiger was only three years old, his father died of apoplexy and he moved to Copenhagen with his mother and sister. His mother supported her family by writing short stories, journals, and cookbooks. In 1882 she also established the Copenhagen Cooking School, the first of its kind.
Fibiger's mother was preoccupied with supporting her family and spent little time with her children's education. Fibiger was sent to an elementary school run by one of his uncles. He was a diligent student who was interested in insects and botany. He spent all of his holidays with another uncle, the Reverend Johannes Fibiger, who helped raise him and supported his education. At the age of 16 Fibiger passed his matriculation exam and began to study zoology and botany at the University of Copenhagen. He paid for his education by teaching and working at the zoology laboratory at the university.
While Fibiger was studying he lived at home with his mother. His mother's cooking school had flourished and expanded to include a restaurant. A distant cousin, Mathilde Fibiger, also the daughter of a physician, came to work at the school as a teacher and an accountant.
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