No European has made it into the top-10 on the American magazine's list.
Foreign Policy says Merkel "finally" seemed to embrace a leadership role in 2012, prescribing a mix of austerity measures, structural reforms and fiscal integration for the European Union.
"She has tacked on mandatory spending cuts to aid packages for Greece, Ireland and Portugal and spearheaded a historic EU deficit-reduction treaty. All along, the much-misunderstood Merkel has insisted on solving the regional crisis with more Europe, not less," the publication said.
13 Europeans in top 100 list
Twelve other Europeans have been considered top global thinkers this year, including European Central Bank President Mario Draghi (20) and Christine Lagarde (27), managing director of the International Monetary Fund.
The only EU politician on the list is Justice Commissioner Viviane Reding (97), recognised "for demanding that Europe's women have a seat at the table."
Foreign Policy said Reding this year pushed an ambitious, if improbable, EU law to create a mandatory 40% quota for women in the boardroom.
Reding has insisted that giving women greater decision-making powers is not only a matter of fairness, but would also be a boon for the economy. The commissioner faced entrenched opposition.
"The law was shot down amid legal concerns in October, though Reding vowed to put forward a modified version. She is keeping at it if only because her proposal is the one serious idea on the table for addressing a gender imbalance that is consequential enough to impact Europe's economic performance - and its values," the American magazine wrote.
The names on Foreign Policy's top-10 global thinkers of 2012 are:
1. Aung San Suu Kyi, the Burmese dissident leader, and Thein Sein, former Burmese military commander and current president.
2. Moncef Marzouki, Tunisia's president.
3. Bill and Hillary Clinton, former US president and outgoing secretary of state.
4. Sebastian Thrun, American computer scientist.
5. Bill and Melinda Gates, billionaire philanthropists.
6. Malala Yousafzai, 15-year-old Pakistani schoolgirl who stood up to the Taliban.
7. Barack Obama, US president.
8. Paul Ryan, US vice presidential candidate on the Mitt Romney ticket.
9. Chen Guancheng, Chinese legal activist.
10. David Blankenhorn, activist, who changed his mind on gay marriage; Narayana Kocherlakota, economist, who changed his mind on inflation; and Richard A. Muller, physicist, who changed his mind on climate change.