Mekonnen came to prominence at the age of eighteen with a silver medal performance in the 5000 m at the 1998 African Championships in Athletics, finishing behind reigning world champion Daniel Komen. He followed this up with a gold and team silver in the junior race and an individual and team bronze medal in the short race at the 1999 IAAF World Cross Country Championships. He put much of his success down to the help he had received from Haile Gebrselassie, who was his training partner and mentor. He ran a world junior record in the 3000 m in Stuttgart, Germany, but this was never ratified as he did not undergo the doping controls necessary for record purposes. He finished seventh in the 5000 m at the 1999 World Championships in Athletics and closed the year with a 1500 metres gold medal at the 1999 All-Africa Games and a win at the Cross Internacional de Venta de Baños. He set an indoor world record of 8:09.66 in the two miles in Birmingham in February. However, Mekonnen only managed sixth place in the short race at the 2000 IAAF World Cross Country Championships, but again he won the team bronze with Ethiopia. He represented his country at the 2000 Summer Olympics, finishing seventh in the semi-finals of the 1500 metres. Competing at his first IAAF World Indoor Championships, he finished seventh in the final of the 1500 m. After this he decided that he would not succeed over distance and permanently switched to the 5000 m, saying: "That’s enough for the 1500. It was tried, it didn’t work." Returning to the cross country championships, he improved to win the team silver at the 2001 edition, although he finished tenth overall. He finished eighth in the 5000 m at the 2001 World Championships in Athletics. He was selected for the 2001 IAAF Grand Prix Final, but he only managed eighth place in the 3000 m final. He also took part in the 5000 m at the 2001 Goodwill Games, just missing out on the medals in fourth. He began taking part in road races and won the Memorial Peppe Greco 10 km. He had his best ever cross country result at the 2002 edition in Belfast, winning a bronze medal for himself and helping Ethiopia to the team silver in the short race. He ran in the QSI 10 km and was second behind Haile Gebrselassie who set a world best for the distance. At the 2003 All-Africa Games, he decided not to defend his 1500 m title and instead opted for the 5000 m and he won the silver medal, just beaten by Kenenisa Bekele. He travelled to Hyderabad in India to compete at the 2003 Afro-Asian Games, where he won the gold in the 5000 m. He took part in the 2003 International Chiba Ekiden and was the fastest runner in the second stage and helped Ethiopia to victory in the fastest ever Ekiden race. He won the Montferland Run 15 km in 2005. From 2008 onwards, he began to focus more on road running competitions. After a long absence from major international competition, he signed up for the 2009 IAAF World Half Marathon Championships. However, he failed to finish the race. He finished second at the Great Scottish Run behind Jason Mbote in late 2009. The following year, he took eighth place at the 2010 Paris Marathon and even though he fell over midway through the race, he recovered to set a personal best of 2:09:01. Further improvement came at the Amsterdam Marathon where, despite finishing in fifth, he ran almost a minute and a half faster than his previous best by completing the race in 2:07:37. He cut another two seconds off his best with his winning time at the 2011 Tokyo Marathon in February. He was runner-up at the Montferland Run that year, being beaten to the title by Philip Langat. He returned to defend his title at the 2012 Tokyo Marathon, but could manage only eighth place on that occasion. on September 22, 2012 he won the heng shui marathon in 2:08.05
