 Nathanael was born as Nesho (Nedyalko) Stoianov (Stankov) Boykikev in village of Kučevište, near Skopje, then Ottoman Empire.He studied at Kučevište monastery, and in 1835 went to study in Samokov.Then continued his education in Prilep, where along with teacher George Samurkashev translate in Bulgarian language the treatise "The Service of Jews and their evil", published in 1839 by Theodosius of Sinai.