As a 19-year-old he won the Four Hills Tournament for East Germany in 1983/84. Weißflog was known as "Floh" (flea in German) due to his slight stature and his light body. That same winter he won the combined World Cup and later the normal hill event at the 1984 Winter Olympics in Sarajevo. The following winter was dominated by Weißflog and the outstanding Finn Matti Nykänen.
The most remarkable part of his career is that he competed at the top level for twelve years. Neither the regime change from East Germany to the unified Germany in late 1990, nor the change in ski jumping techniques from the parallel technique to the V-style around 1993 stopped his success. In 1994 he won two gold medals in the individual large hill and team large hill events at the 1994 Winter Olympics in Lillehammer, ten years after his first Olympic victory. He finished his career in 1996 by becoming the first ski jumper to win the combined Four Hills Tournament four times. Only the Finn Janne Ahonen has surpassed that record by winning the Four Hills Tournament five times. He had also earned five-second place finishes in the competition over the course of his career. After this achievement he retired from professional sport.
At the FIS Nordic World Ski Championships, Weißflog won two golds in the individual normal hill (1985, 1989), three silvers in the individual large hill (1989) and team large hill (1984 and 1995), and four bronzes in the individual large hill (1991, 1993) and team large hill (1985 and 1991). He also won two medals at the FIS Ski Flying World Championships with a silver in 1985 and a bronze in 1990.