After moving to Zagreb, where he graduated at the Institute of Physical Culture, he represented Dinamo from 1958 to 1966. Afterwards, he played abroad, for Wiener SK and Austria Vienna in Austria and Gent in Belgium. His club career ended in 1968.

As an international for the former Yugoslavian national team, he made his debut against Hungary in Belgrade in 1961, and was selected for the World Cup in Chile a year later, where he was included in the team of the tournament. Vlatko Marković was capped 16 times.

NK Zagreb offered him first job as a coach. Later, he became the head coach of the Yugoslavia U-23 and won the European Championships. His list of teams coached also include Standard Liege, Nice, Rapid Vienna, Hajduk Split, and Dinamo Zagreb on several occasions (1978 - 1980, 1983, 1990 - 1991 and 1992).

In 1993, Marković was the head coach of the Croatian national football team for the friendly win against Ukraine in Zagreb (3:1).

From 1998 to 2012, Marković held the office of the President of the Croatian Football Federation. He was succeeded by current president Davor Šuker and appointed as honorary president of the CFF. Moreover, he was a FIFA instructor, a member of the FIFA Coca-Cola Programme, vice-president of the CFF, a president of the CFF Technical Committee, a member of the UEFA Technical Development Committee, a member of the FIFA National Associations Committee, a member of the FIFA Goal-project Committee and president of the UEFA Technical Committee.

Marković was awarded on multiple occasions. His awards include, among others, the Croatian Olympic Committee Matija Ljubek Award, Franjo Bučar National Sports Award and French national medal for promotion of football in France and abroad.

Vlatko Marković passed away on September 23rd, 2013 in Zagreb.