Her place on the Kenyan world cross country team looked uncertain in 2009 as head coach Julius Kirwa dismissed her chances, saying she had run too many races that season. Cherono replied by taking the lead immediately at the Kenyan Trials and winning the junior race by a margin of thirteen seconds. At the 2009 World Cross Country Championships in Amman, Cherono engaged in a race-long duel with Genzebe Dibaba in the junior race. Cherono took the lead in the final stages but a difficult stretch with a 40-metre climb enabled Dibaba to overtake her and Cherono ended up with the silver medal. At the 2009 African Junior Athletics Championships, Cherono eased to the 3000 m title by some 13 seconds but found herself beaten again by Genzebe Dibaba in 5000 m race, finishing with the silver medal. She competed on the senior track circuit that year and was third at the Rieti IAAF Grand Prix, recording a personal best of 8:44.67 for the 3000 m. She took third for a second time at the Memorial van Damme in September, recording personal bests in the 1500 metres and 2000 metres and beaten only by reigning world champions Gelete Burka and Vivian Cheruiyot.