He was the youngest son of Friedrich Wilhelm I, Duke of Saxe-Weimar, and Anna Maria of the Palatinate-Neuburg, his second wife.

Shortly after his birth, Friedrich Wilhelm II and his older brothers inherited Saxe-Altenburg as co-rulers under the guardianship of the Electors of Saxony Christian II and John George I until 1618, when his older brother John Philip assumed the government of the duchy and the guardianship of his younger siblings.

Friedrich Wilhelm II was only a nominal ruler until the death of John Philip (1639), when he began his personal reign over Altenburg.

At Altenburg Castle on 18 September 1638 Friedrich Wilhelm II married his first wife, Sophie Elisabeth, the only daughter of Christian William of Brandenburg.

In Dresden on 11 October 1652 Friedrich Wilhelm II married secondly Magdalene Sibylle of Saxony, Dowager Crown Princess of Denmark and daughter of his former regent, the Elector John George I.