Born in Machakos, he began running seriously around 2004 in the hope he could make a living out of the sport. Ndiku made his international debut at the 2007 World Youth Championships in Athletics, coming fourth in the 2000 metres steeplechase event. His technique was poor and his coach, Paul Mutwii, turned to Boniface Teren, the Kenyan national steeplechase coach, for help. Working with Teren, Ndiku's technique over the barriers greatly improved and one year later he won the gold medal at the 2008 World Junior Championships in Athletics, beating Uganda's Benjamin Kiplagat who had built up a sizeable lead in the early stages. Ndiku's winning time of 8:17.28 minutes was enough to rank the 16-year-old in the top 25 athletes in the world that year, as well as being the fastest ever recorded by a youth category athlete. His flat speed also improved, as he won the 1500 metres at the Commonwealth Youth Games that year. He also competed in Japan that year. After signing up with the Hitachi Cable corporate running team, he set track bests of 7:54.04 minutes for the 3000 metres, 13:21.17 minutes for the 5000 metres and 28:08.28 minutes for the 10,000 metres.