Born in Punkaharju, Hänninen debuted in the Finnish Rally Championship in 2003, finishing eighth in the Group N class. In 2004 he won that class title driving a Honda Civic Type R, and the following year he placed second in Group N with a Mitsubishi Lancer Evolution VI.
Hänninen's first WRC event was the 2006 Swedish Rally, where he won the Group N class in a Lancer Evolution IX and placed fifteenth overall. He repeated as the fastest Group N driver at the Rally d'Italia Sardegna and collected his best overall WRC result of ninth at the Rally New Zealand. A debut in a World Rally Car in Finland ended in exclusion after he was found not to be wearing the correct fireproof underwear.
In 2007, Hänninen ran a full six-event PWRC programme in the Lancer Evolution IX, initially winning the Swedish Rally before disqualification for non-homologated fuel pumps. He took two further podiums — second in Britain and third in Argentina — and finished fifth in the PWRC standings. He also contested three WRC events in a Mitsubishi Lancer WRC05, taking his first outright WRC championship point with an eighth place at the Rally d'Italia Sardegna.
In 2008, Hänninen won both the Swedish Rally and Rally Finland in the PWRC, also claiming his first Super 2000 event victory at Rally Russia in a Peugeot 207 S2000.
For 2009, Hänninen moved to the Intercontinental Rally Challenge driving a Škoda Fabia S2000, winning in Russia for the second consecutive year and finishing sixth in the championship. He continued with Škoda for 2010, delivering his most successful season to that point: three victories in Argentina, Sardinia, and Scotland, along with four second places and three third places, giving him the 2010 IRC championship title. He also won the S-WRC class at Rally Finland that year.
In 2011, Hänninen competed in both the IRC and the S-WRC for Red Bull Škoda. He clinched the Super 2000 World Rally Championship title at the Rally Catalunya, becoming S-WRC champion with co-driver Mikko Markkula.
His WRC career at the top level continued into 2013, when he set his first-ever stage win in the World Rally Championship at the Monte Carlo Rally, topping stage nine. Later that year, Hyundai signed Hänninen as an official test driver to help develop the new Hyundai i20 WRC ahead of the manufacturer's return to the championship.
Juho Hänninen's double championship season of 2010–2011 — IRC champion followed immediately by S-WRC champion — remains one of the more impressive streaks in sub-WRC rally competition. His role in developing the Hyundai i20 WRC extended his influence beyond his competitive record, contributing to Hyundai's eventual success as a top-tier WRC manufacturer.