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The case for having a founder run the business

February 7, 2013, 12:00 PM UTC

FORTUNE — The paradox faced by the CEO of any startup is that if he makes the business succeed, he will probably be fired. Conventional wisdom holds that once a business begins to grow, a founder ought to be replaced by a professional manager — someone who has had experience building a company.

Statistically speaking, this makes sense. Harvard Business School professor Noam Wasserman has spent the past decade studying the impact a founder has on a company. In a study of 460 American startups, he found that on average those in which founding CEOs remained the top decision-makers were less valuable than those managed by outside CEOs. Simply put, the skills needed to invent a new product or service are different from those needed to manage a business, and few people possess both.

But that’s the rule on average. If you’re looking for people to hit it big, you’d be smart to bet on founders. Throughout history, the most successful companies have been led by their passionate creators. Nearly every person Fortune has ever named Businessperson of the Year — people like Amazon’s Jeff Bezos and Netflix’s Reed Hastings — has been a founder, and so have most of the nominees. Industry’s most iconic business figures include founders like Wal-Mart’s (WMT) Sam Walton, Harpo Productions’ Oprah Winfrey, Nike’s (NKE) Phil Knight, and perhaps most famously, Apple’s cantankerous genius, Steve Jobs. While not every founder will be as efficacious as Jobs, nearly every company that has come close to Apple-like levels of success is run by a founder.

Some startup investors have taken note of this. Investors from Digital Sky Technologies’ Yuri Milner to Andreessen Horowitz have built their investment strategies on “sticking with the founders,” as Milner has said. The Founders Fund, which includes Peter Thiel as co-founder, has invested $1 billion in more than 100 companies without ever firing a founder. Incubators like Paul Graham’s Y Combinator accept new startups based not just on the quality of their ideas, but also on the skills and enthusiasm of the teams that pitch them. Sure, some of it is good marketing: An investor is more likely to get in on a deal if he promises to support the company’s founder. But, as startup whisperer Reid Hoffman — a founder himself — wrote in a recent essay on the topic, “The new received wisdom [among tech investors] is that the best entrepreneurs can stay CEO through the entire growth cycle of the company.”

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Why bet on founders? They dream up new things. Trailblazer Tony Fadell rethought the method for controlling home temperatures with Nest, a thermostat that looks more like an iPod. Anya Fernald rethought the supply chain for cultivating and delivering healthy food, bringing us grass-fed meat at scale at Belcampo. Those who back founders will argue that while you can sometimes teach a dreamer to be a strong business operator, you can rarely teach a businessman to dream.

These entrepreneurs also have a moral authority over their products. “Founders have the credibility to reinvent their business without losing the support and trust of the old-culture loyalists,” says Yale School of Management professor Jeffrey Sonnenfeld. An innovative company must make decisive bets. At times, it must act quickly to pilot a new business, even if it cuts into the main business. Founders are often best positioned to make these bold moves because they understand the larger vision for the company better than anyone else. For example, when Reed Hastings founded Netflix (NFLX), the company put Blockbuster out of business by delivering its red-enveloped DVDs by mail. Then, in 2007, Hastings began a streaming service that eventually disrupted his core business. Though the fate of Netflix in today’s market remains unclear, this hasty and decisive forward-thinking move positioned Netflix to weather a massive technology shift.

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Perhaps most important, founding CEOs take the long view. While CEOs hold their job on average for just eight years, founding CEOs often aim to run their companies for life and to build a legacy for themselves while changing the world with a new product or service. As Ben Horowitz, another trailblazer, writes in his seminal essay on founders, “Their emotional commitment exceeds their equity stake.” Consider the online bookstore that Jeff Bezos started in 1994, Amazon (AMZN). Though the company went public in 1997, Bezos followed an unusual business model that unfolded slowly over the course of four or five years. Analysts and investors complained. But even as the dotcom bubble burst, Amazon became profitable, and Bezos has continued to pilot the company into ever-expanding opportunities.

Although Fortune’s Trailblazers are early in their careers — their companies are all less than five years old — they possess a commitment to long-term leadership that cause many, like Kickstarter CEO Perry Chen or Airbnb CEO Brian Chesky, to vow never to sell the company.

Most founding CEOs will fail, simply because most startup ventures fail. Those who do find success may discover that it is fleeting: Many brilliant founders will, like BlackBerry’s (BBRY) Michael Lazaridis or Yahoo’s (YHOO) Jerry Yang, miss a turn in the market and see their business decline. But there will be a few Henry Fords and Estée Lauders, men and women who see the world not for what it is but for what it can become, and build a company to move us all in that direction. When the future historians of the 21st century call these folks out, it’s a good bet they will be founders.

This story is from the February 25, 2013 issue of Fortune.