Werknesh began her 2003 season with a win at the Antrim International Cross Country and then went on to take the women's long race title at the 2003 IAAF World Cross Country Championships. She won the silver medal in the 10,000 m at the 2003 All-Africa Games, finishing behind fellow Ethiopian Ejegayehu Dibaba. Her season peaked at the 2003 World Championships in Athletics where she set a 10,000 m personal best of 30:07.15 minutes to secure the runner-up position behind Ethiopian veteran Berhane Adere who broke the African record for the event. The following year she came fourth in the event at the 2004 Athens Olympics. She also won the long race bronze medal at the 2004 IAAF World Cross Country Championships, as well as taking fourth in the short race.