Jakše was born in 1959 in Ljubljana. After his studies at the Ljubljana Faculty of Arts, he studied at the painting department of the Ljubljana Academy of Fine Arts (1982/83-1988, under Prof Metka Krašovec). He made several study trips to New York (October-December 1998, on scholarship from the Slovene Ministry of Culture), Vienna (November 2000) and Paris (2004). He held his first solo exhibition in 1991 at Galerija Equrna (again in 1993 and 1998). Important solo exhibitions of his paintings include exhibitions at Galerija Škuc (1992, 2005), Cekinov Grad (1995), Galerija Likovnih Umetnikov Slovenj Gradec (1998/99), Grad Kodeljevo (2003/04) and Kibela in Maribor (2004).
He has published several catalogues and books about his work: Marko Jakše (1991), Marko Jakše. Bukanje (1993), Marko Jakše (1995), Marko Jakše: 91-94 (1998).
He works as a painter and designer. In 1992 he received the Zlata Ptica Award.