In the 1990s, Lončarević was also in charge of several other Croatian teams including NK Zagreb, Marsonia, Slaven Belupo and Hrvatski Dragovoljac.
In the summer of 2000, after a short spell with Marsonia, Lončarević was appointed head coach at Čakovec, who just won their first promotion to the Croatian first division at the time, and led the club through the first part of the 2000–01 season.
After this first spell with the Libya national team, Lončarević went on to take charge of Dinamo Zagreb in November 2004 and stayed there until the end of the season.
However, after Libya lost to Egypt and Ivory Coast in their first two group matches at the tournament, chairman of the Libyan Football Federation, Gamal Al Gaafari, announced that the coach will be relieved of his duties after the last group match against Morocco, which ended in a goalless draw.
However, on 6 October 2009, barely 5 weeks after the start of the Albanian Superliga, Lončarević gave his resignations[3] without citing any reasons why he did that.