The alliance said in a statement the ambassadors of the 19 NATO nations agreed that De Hoop Scheffer will succeed Britain's Lord Robertson, who is stepping down in December after serving his four-year term.
"As foreign minister, he has impressed all his colleagues with his judgment and grasp of the issues," Robertson said in the statement.
"These are challenging times for NATO ... and I am delighted that we have found the right man to ensure NATO remains the world's most successful defense alliance."
Canada and France held up an agreement on De Hoop Scheffer last week.
France wanted more time to discuss the issue and Canada stuck by its candidate, Canadian Finance Minister John Manley, who was the Dutchman's main rival for NATO's top job.
However, Manley failed to rally support from European allies reluctant to relinquish their traditional hold on the secretary-general's post.
De Hoop Scheffer is seen as a bridge maker between the United States and those European allies whose opposition to the Iraq war earlier this year prompted NATO's deepest split for years.
The Dutch government supported the war but avoided taking a high profile in the dispute with NATO's anti-war nations led by France and Germany.
The center-right government, which De Hoop Scheffer joined as foreign minister last year, has maintained the Netherlands' traditional support both for closer integration among European nations and a strong trans-Atlantic alliance.
Although relatively inexperienced at the highest levels of government, De Hoop Scheffer, 55, has impressed his NATO colleagues with a no-nonsense approach and commitment to modernizing the alliance.
A career diplomat turned politician, De Hoop Scheffer served at the Dutch mission to NATO in the 1980s, before entering the Dutch parliament where he rose to become leader of the center-right Christian Democrats.
De Hoop Scheffer met with U.S. President George W. Bush during an official visit to Washington last week, an event Dutch media called an American examination to determine if the Dutchman is suited for the post. Diplomats said the meeting went well and the United States backed his candidacy.
Talks to select a new leader among the 19 allies are notoriously secretive. Candidates rarely declare their interest publicly and governments are very discreet about who they support. However, several nations have expressed open support for De Hoop Scheffer in recent weeks.
Since NATO's founding in 1949, the alliance's top civilian post has been held by a European, while a U.S. general serves as the supreme allied commander.
Several European figures were mentioned a possible replacements for Robertson since he announced his intention to step down in February, including Italian Defense Minister Antonio Martino, Portugal's European Union commissioner Antonio Vitorino and Norway's Defense Minister Kristin Krohn Devold, who would have been the first woman to hold NATO's top job.
Robertson, a former defense minister in Britain's Labor government, is to become a deputy chairman of telecommunication's group Cable & Wireless PLC.
De Hoop Scheffer's appointment marks the third time a Dutchman takes the NATO helm. Dirk Stikker served as secretary general from 1961-1964 and Joseph Luns and from 1971-1984.