Wenger topped a table complied by the 'International Football Federation of History & Statistics' (IFFHS) - an organisation recognised by FIFA.
The 61-year-old, whose team have not won any silverware in six years, earned 156 points while Ferguson was second (148) and Real Madrid's Mourinho followed in third (135).
The result was calculated by combining the results of the previous 10 years of the organisation's manager-of-the-year, which in 2010 was won by Spain's World Cup-winning coach Vicente Del Bosque.
According to the IFFHS it was Wenger's consistency in the 10-year period that earned him the award.
Their website stated of the man who moved to Arsenal from Japanese club Nagoya Grampus Eight in 1996: "Although the Frenchman has until now never won the annual vote, he has been among the best-placed coaches every year.
"It is admirable how he has repeatedly molded young players into an attacking and technically brilliant way of play."
IFFHS - Top 10 managers 2001-2010
1. Arsene Wenger France 156
2. Sir Alex Ferguson Scotland 148
3. Jose Mourinho Portugal 135
4. Fabio Capello Italy 120
5. Guus Hiddink Holland 112
6. Carlo Ancelotti Italy 108
7. Luiz Scolari Brazil 101
Marcelo Bielsa Argentina 101
9. Rafael Benitez Spain 97
10. Marcello Lippi Italy 88