Warner Bros. Discovery lost money last year. Its CEO got a $50 million payday.

Last year, CEO David Zaslav received pay valued at $49.7 million, a 27% increase from 2022, the company said in a securities filing Friday. That is more than three times as much as the $15.6 million median pay of S&P 500 CEOs whose compensation had been disclosed through late March.

The company, home of the Warner Bros. movie studio, the Max streaming service and cable channels including HBO, CNN, TNT and Food Network, posted a smaller net loss—but also narrower revenue—last year. But Zaslav’s stock award was tied to another metric: free cash flow, which nearly doubled to $6.16 billion last year as the company moved aggressively to pay down debt.

Zaslav has been cutting costs ever since he took the helm of the company, the result of a merger between  Discovery and AT&T’s WarnerMedia. That effort continued in 2023 through staff reductions and tighter budgets on content spending and marketing. The company also wrote off projects, such as the movie “Coyote vs Acme."

Overall, Zaslav’s compensation included a $3 million salary, $23 million in stock awards tied to cash flow and a guaranteed $22 million cash bonus. He also got perks, including personal security at his various residences valued at more than $700,000, and $768,000 for use of the corporate jet.

Free cash flow reflects funds available to a company after operating expenses and capital investment, and is one measure investors use to gauge a company’ health. For compensation purposes last year, Warner Bros. Discovery disregarded about $1 billion in cash flow that resulted from the 2023 strikes by writers and actors, which temporarily reduced movie and television production expenses.

In 2022, Zaslav’s equity award was tied to multiple performance metrics, including measures of company revenue and subscriber volume, as well as cash flow, securities filings show.

Like other entertainment conglomerates, Warner Bros. Discovery has faced challenges across many fronts in the past few years. Cord-cutting and an extended advertising slowdown have taken a significant bite out of its cable networks.

The movie studio’s performance last year was so-so. While “Barbie" was a megahit, there were several pricey flops, including “The Flash," “Blue Beetle" and “The Color Purple."

While its Max streaming service is profitable, Warner Bros. Discovery also includes the licensing of Warner Bros. content to other services such as Netflix as part of the revenue for its direct-to-consumer unit that houses the platform.

The company’s stock has lost about two-thirds of its value since the merger was completed in April 2022, though it ended 2023 20% higher than it ended 2022. The S&P 500 index rose 24% last year.

The second-highest compensated corporate officer at Warner Bros. Discovery was JB Perrette, who oversees streaming and games, with a package valued at $20.1 million. Chief Revenue and Strategy Officer Bruce Campbell’s 2023 compensation was valued at $18.3 million and Chief Financial Officer Gunnar Wiedenfels had a package of $17 million.

By emphasizing cash flow so heavily, Warner Bros. Discovery shifted Zaslav’s pay away from the mainstream for the biggest U.S. public companies, data from ISS-Corporate, a unit of Rockville, Md.-based Institutional Shareholder Services, show.

Over the past five years, the share of companies using sales or stock-market metrics has grown somewhat, while other measures have stayed fairly flat. Companies can use multiple performance measures when setting pay.

Of S&P 500 companies reporting 2023 pay details so far, about 70% used earnings to help set executive pay, and about the same share relied at least in part on stock-price performance or shareholder returns, ISS-Corporate found. Around half took sales into consideration, and just under half relied on other returns or margins. Only about 29% used a measure of cash flow.

Write to Joe Flint at Joe.Flint@wsj.com and Theo Francis at theo.francis@wsj.com