As the third born son and with primogeniture in Saxe-Lauenburg Francis II made a military career in imperial services. In 1571 his highly indebted father Francis I resigned in favour of his eldest surviving son Magnus II, who had promised to redeem the pawned ducal demesnes with funds he gained as Swedish military commander and by his marriage to a Swedish princess. However, Magnus did not redeem pawns but further alienated ducal possessions, which ignited a conflict between Magnus and his father and brothers as well as the estates of the duchy, further escalating due to Magnus' violent temperament. In 1573 Francis deposed Magnus and reascended to the throne. The following year Magnus hired troops in order to take Saxe-Lauenburg with violence. Francis II, an experienced military commander, and Duke Adolphus of Holstein-Gottorp, then Lower Saxon Circle Colonel, then helped Francis I to defeat Magnus. In return Saxe-Lauenburg had to cede the bailiwick of Steinhorst to Adolphus' Holstein-Gottorp in 1575. Francis II again helped his father to inhibit Magnus' second military attempt to overthrow his father in 1578. Francis I then made Francis II his vicegerent actually governing the duchy. In 1581 – shortly before he died and after consultations with his son Prince-Archbishop Henry of Bremen and Emperor Rudolph II, but unconcerted with his other sons Magnus and Maurice – Francis I made his third son Francis II, whom he considered the ablest, his sole successor, violating the rules of primogeniture. This severed the anyway difficult relations with the estates of the duchy, which fought the ducal practice of growing indebtedness. Francis only officiated as administrator of Saxe-Lauenburg. Magnus appealed at Rudolph II, who in 1585 finally decided in favour of Francis II, as agreed with Francis I in 1581. Francis II, who meanwhile had won his brother Maurice, by sharing the reign with him, lured Magnus into a trap and captured him later in 1585. Francis and Maurice kept their brother imprisoned for the rest of his life, mostly in the castle of Ratzeburg, where he died in 1603. The violation of the primogeniture, however, gave grounds for the estates to perceive the upcoming duke as illegitimate. This forced Francis II into negotiations, which ended on 16 December 1585 with the constitutional act of the "Eternal Union" of the representatives of Saxe-Lauenburg's nobility and cities, Lauenburg upon Elbe and Ratzeburg, then altogether constituted as the estates of the duchy, led by the Land Marshall, a hereditary office held by the family von Bülow. Francis II accepted their establishment as a permanent institution with a crucial say in government matters. In return the estates accepted Francis II as legitimate and rendered him homage as duke in 1586. . Abbreviated inscription: V. G. G. F. H. Z. S. E. V. W. The relations between estates and duke improved since Francis II redeemed ducal pawns with money he had earned as imperial commander. Already earlier in 1585, after consultations with his brother Prince-Archbishop Henry, Francis II decreed a constitution for the Lutheran church of Saxe-Lauenburg. In 1592 Francis II granted his second wife Maria of Brunswick-Lüneburg a manorial estate near Schulendorf. Starting in 1608 Francis extended the existing house to a castle with a large garden, called Franzgarten or Franzhof, in the end the name Franzhagen prevailed. Francis II left workers, employed in castle constructions, short. Till his death he used the castle, which his widow Mary then used until she deceased in 1626. In 1608 Francis II acquired the minting regal for Saxe-Lauenburg. After Maurice had died in 1612, Francis became the sole ruling duke. In 1616 the ducal residential castle in Lauenburg upon Elbe, started in 1180–1182 by Duke Bernard I, burnt down. Francis then also used another residence in Neuhaus. Francis died in 1619 and was buried in the ducal family crypt in the St. Mary Magdalene Church in Lauenburg upon Elbe, his widow Mary, died in 1626, was buried alongside him.
On 10 November 1582 Francis II married in Wolfenbüttel his second wife, Maria of Brunswick-Lüneburg, daughter of Duke Julius, Duke of Brunswick-Lüneburg, making her the new consort. Mary and Francis had 14 children, of whom the following 12 reached adulthood:
