He was born in Torgau, the eldest (but fourth in order of birth) surviving son of Friedrich Wilhelm I, Duke of Saxe-Weimar and Anna Maria of the Palatinate-Neuburg, his second wife.

Because of this, his uncle Johann (more interested in natural sciences and art than politics) took over his guardianship and the regency of his inheritance; but shortly after he took all the duchy of Saxe-Weimar into his own hands.

In 1638, he received the towns of Coburg, Bad Rodach, Römhild, Hildburghausen and Neustadt, according to the divisionary treaty between him and the branch of Saxe-Weimar after the death of the duke John Ernest of Saxe-Eisenach without surviving issue.

Before his death, he made a will, when he declared his daughter the general heiress of the branch of Saxe-Altenburg, only in case of extinction of the male issue of the family.

Johann Philipp died in Altenburg, and was succeeded by his younger and only surviving brother, Frederick William II.