She started out in middle-distance events, running in the 800 metres at the 2004 World Junior Championships and then winning a 1500 m silver medal at the World Youth Championships in Athletics the following year. She won the bronze medal in the 1500 m at the 2005 Asian Championships in Athletics and went one better at the 2006 Asian Games by taking the silver medal in Doha. Kobayashi moved up to specialise in longer distances and ran the 5000 m at the 2008 Beijing Olympics after becoming the Japanese national champion in the event.