The article, which is just over 1,000 words long, seeks to explain the reasoning behind Facebook's targeted advertising model and clear up confusion around its handling of people's personal information.
Zuckerberg said that the lack of a price tag on Facebook's service has become an area of "complexity" when it comes to trying to understand its business model.
"In an ordinary transaction, you pay a company for a product or service they provide," he wrote. "Here you get our services for free — and we work separately with advertisers to show you relevant ads. This model can feel opaque, and we're all distrustful of systems we don't understand."
Zuckerberg added: "Sometimes this means people assume we do things that we don't do. For example, we don't sell people's data, even though it's often reported that we do."
The company has become the target of much criticism over the way it handles people's personal information in the wake of revelations last year that it allowed political consultancy Cambridge Analytica to gain access to the data of 87 million people.
The fact that the column was published in the WSJ appears to be a significant move, given that the newspaper's core readership includes business professionals and investors. Facebook's stock became increasingly unloved by investors last year — shares have fallen around 20 percent since Mar. 17, the day on which initial reports of the leaking of data to Cambridge Analytica were published.
Zuckerberg said Facebook selling user information on to advertisers would be "counter to our business interests, because it would reduce the unique value of our service to advertisers." He said the firm has a "strong incentive" to protect users' data.
Facebook's claim that it doesn't sell people's data has been disputed by academics and privacy advocates. The firm says that it only sells targeted advertising, a model of online marketing that essentially optimizes ads based on a user's interests and clicking habits.
Michal Kosinski, an assistant professor at Stanford University, said last year that the company's claim it does not sell user data is "like a bar's giving away a free martini with every $12 bag of peanuts and then claiming that it's not selling drinks."
"Rich user data is Facebook's most prized possession, and the company sure isn't throwing it in for free," Kosinski said in a New York Times opinion piece.
Facebook's chief said that, while it does collect information on users, it lets them control how that information is used for ads and doesn't use the data without first obtaining consent, in compliance with the European Union's GDPR data protection law. GDPR states that companies that hold data on users must obtain explicit consent, and that they should give people the ability to access data held on them and find out why it's being used.
Zuckerberg was grilled over its data practices by politicians in both U.S. Congress and the European Parliament. However, he declined an invitation from British lawmakers to take questions several times, instead sending the firm's technology chief and a policy executive.
Facebook was hit with a £500,000 ($650,000) fine by the U.K.'s privacy watchdog last year for failing to protect user data. It hasn't been the only firm to be dealt regulatory penalties for data protection violations, however — Google was sanctioned 50 million euros ($57 million) by the French data authority for an apparent breach of GDPR.
Zuckerberg said in the WSJ column that he welcomed data protection regulation "across the internet that would be good for everyone." He said such regulation should stress "transparency, choice and control."