John Frederick of Schleswig-Holstein-Gottorp (born 1 September 1579 in Gottorp, a part of today's Schleswig; died 3 September 1634 in Altkloster , a part of today's Buxtehude) was the Lutheran Administrator of the Prince-Archbishopric of Bremen, the Prince-Bishopric of Lübeck and the Prince-Bishopric of Verden.
His parents were Adolf I, Duke of Schleswig-Holstein-Gottorp and Christine, Landgravine of Hesse-Cassel. John Frederick and Anna Dobbel from Bremervörde, the Bremian prince-archiepiscopal residence, had two children: Friedrich and Christine. In 1621 Ferdinand II, Holy Roman Emperor, legitimated them and ennobled them as von Holstein.
After John Frederick's brother John Adolf succeeded their brother Philip, Duke of Schleswig-Holstein-Gottorp as Duke of Schleswig-Holstein-Gottorp, the Bremian Chapter feared John Adolf would integrate the Prince-Archbishopric of Bremen into his inheritable ducal monarchy. The Chapter demanded that John Adolf would resign, what he did in 1596 in favour of John Frederick. In 1607 John Adolf also handed over the Prince-Bishopric of Lübeck to his brother.
At the beginning of the Thirty Years' War John Frederick and his prince-bishoprics of Bremen and Lübeck maintained neutrality, as did most of the territories in the Lower Saxon Circle.