Francis Charles was a son of the Duke Francis II of Saxe-Lauenburg from his second marriage to Maria of Brunswick-Lüneburg. In 1619, Francis Charles and his brothers confirmed in an inheritance contract that their elder half-brother Augustus would inherit all of Saxe-Lauenburg. Francis Charles went into military service, and after serving in various armies, he eventually joined the Protestant army of Count Ernst von Mansfeld. With this army, he fought in Bohemia against Emperor Ferdinand II. Three of his brothers served in the imperial army opposing him. In 1623, Francis Charles' elder brother Julius Henry came to a reconciliation with the Emperor. At a meeting of Protestant Princes in Lauenburg upon Elbe in 1625, it was decided to put Lower Saxony under the protection of King Christian IV of Denmark against the Emperor and his Catholic League. Francis Charles recruited a new regiment for the Danish King and quartered it in his brother's neutral Saxe-Lauenburg, where his troops took a hostile stance. After Christian IV was defeated, Francis Charles asked Wallenstein to help him seek another reconciliation with the Emperor. On 19 September 1628 Francis Charles married Agnes of Brandenburg, widow of the Duke Philip Julius of Pomerania-Wolgast. Again with the help of Wallenstein, his brother Francis Julius achieved, that his wife was allowed keep her jointure, the district of Barth. After King Gustavus II Adolphus of Sweden had landed in Pomerania in 1630, Francis Charles entered his service as a colonel. Francis Charles was captured at the residence of his brother Augustus in Ratzeburg by the imperial general Pappenheim, but was soon back in Swedish service as a colonel. After the death of Gustavus Adolphus, Francis Charles switched sides and joined the army of the Electorate of Saxony. This allowed him to reconcile with the Emperor once again. In 1637, Francis Charles converted to Catholicism and entered the imperial service as a major general. After the death of his first wife, and after imperial mediation Francis Charles married on 27 August 1639 in SopronCatherine of Brandenburg, the very rich widow of the Transylvanian prince Gábor Bethlen. His second wife sold all her Hungarian possessions and moved with her husband to Germany, where she died in 1649. Francis Charles remarried in 1651 Countess Elisabeth Christine of Meggau, widow of the Baron Adolf Christoph of Teuff. After leaving the military service he toured Italy. He died in Saxe-Lauenburgian Neuhaus and, despite his three marriages, he left only childrenborn out of wedlock.
