Weidlinger started his career as a specialist in the 3000 metres steeplechase and he just missed out on a medal at the 1996 World Junior Championships in Athletics, finishing fourth in the final. He won his first championship medal the following year, by winning the steeplechase race at the 1997 European Athletics Junior Championships. He began representing Austria in cross country running competitions and after winning a silver medal in the junior race at the 1997 European Cross Country Championships, he stepped up to the senior ranks for the 1998 edition and was fourth, just a second behind Driss El Himer. After winning the gold medal at the 1999 European Athletics U23 Championships, he attended his first global senior championships – the 1999 World Championships in Athletics. He reached the steeplechase final and finished in ninth position with a national record time of 8:10.83. He improved upon this the following year by taking eighth place in the same event at the 2000 Summer Olympics.