Born in Antwerp, he was the eldest son of spice and drug trader Emil Mayer and his wife Henriëtte Isabelle Joanna (1838–1920).
Wealthy like her husband (she was bequeathed five castles over the course of her life), Henriëtte was an art collector and daughter to the gin distiller Jean-Felix van den Bergh, who lived in kasteel Maxburg in Meer.
Frederik inherited millions of francs on his father's death, investing it in art, including many old master paintings and built up a renowned knowledge of art history, particularly Pieter Bruegel the Elder and Cornelis de Vos, owning five works by the latter artist.
He was promoted to the Belgian hereditary nobility in 1888, with the inheritable title of "ridder" (knight), but he died unmarried from a riding accident in Antwerp aged only 43.
He left it to his mother, who fulfilled his wishes and founded the Museum Mayer van den Bergh.