In 1819 Aarestrup became a student, and continued to study medicine at the University of Copenhagen, graduating as a physician in 1827. That same year he married his 15 year old cousin Caroline Aagard and together they settled in Nysted on the Danish island Lolland, where he would have his practice. It was later found out that he had actually fathered an illegitimate daughter with his landlords wife during his studies in Copenhagen, which naturally put strains on his relations with Caroline, but even so, he made provisions for this daughter also, besides from fathering no less than 12 children with his wife.