Zersenay failed to make the podium for a second time at the 2006 World Cross Country Championships, but his fourth-place finish headed the Eritrean team towards silver medal in the team competition. The following month, Zersenay overcame both Fabiano Joseph and Boniface Kiprop to win the Great Manchester Run. He sprinted to the line with a finishing time of 27:36; an Eritrean record and the second fastest that year. In August that year, he significantly improved his 10,000 m best at Memorial Van Damme; his time of 26:37.25 knocked almost thirty seconds off his previous mark to make him the 8th fastest person ever, but he still finished behind the emerging Micah Kogo who ran the tenth fastest ever time. A new best of 59:16 by Zersenay at the Rotterdam Half Marathon equalled Samuel Wanjiru's course record and boded well for the upcoming championship race.