Jennifer McNary, a stay-at-home mother, was desperate to find a medicine that might spare her two sons an early death from a rare form of muscular dystrophy.

Chris Garabedian, the chief executive of a pharmaceutical firm, was desperate to find a profitable drug that would reverse his company’s slow fall.

They met in June 2012 at a conference on Duchenne muscular dystrophy and joined forces, often behind the scenes and with little public disclosure, in a yearslong mission to push the government to approve a drug to treat DMD, as it is known.

At the time, it wasn’t at all clear the firm’s drug worked. Faced with government skepticism, a consultant to Mr. Garabedian’s company helped Ms. McNary and other parents prepare slickly packaged testimony to convince the Food and Drug Administration that the drug was helping their sick children, according to parents, company managers and the consultant.

Jennifer McNary and her sons Max, left, and Austin during the fall of 2015 in Pembroke, Mass. Photo: Kayana Szymczak

The company, Sarepta Therapeutics Inc., leveraged the emotional appeal of the parents’ stories. Without that, the drug—eteplirsen—likely wouldn’t have been approved, said stock analysts, investors and people close to the matter.

An FDA advisory committee voted 7-6 last year to oppose the drug’s approval, a position later overruled. The Wall Street Journal found that a majority didn’t know how Sarepta’s consultant had guided the patients’ families.

“More might have voted no if they were aware,” said Dr. Bruce Ovbiagele, a committee member, when he learned the role the company consultant played in helping parents prepare for FDA hearings.

Relationships between companies and advocacy groups are important to know about, said Dr. G. Caleb Alexander, co-director of the Johns Hopkins Center for Drug Safety and Effectiveness, who served as chairman of the FDA’s advisory committee. “The advisory committee received little information about how that played out in the development of eteplirsen.”

Companies that need Washington have turned to new, often untraceable tools—including hidden involvement with grass-roots organizations—to lobby decision makers and help sway public opinion. Many of these emerging tactics fall outside the government’s longstanding definition of lobbying and remain masked to both officials and the public, making it hard to know how companies are interacting with the people charged with running the country.

Eteplirsen’s drug application coincided with a shift at the FDA to give a larger role to patient families and advocacy groups. The change helped propel the drug-campaign effort by Sarepta and parents.

“The FDA’s regulatory decision-making on medical products is science-based and involves the careful evaluation of risks and benefits for the drug at issue and is informed by science, medicine, policy and judgment,” an agency spokeswoman said.

This account of the drug’s FDA application is based on interviews with parents, company officials, investors and current and former FDA officials.

When Ms. McNary first talked with Mr. Garabedian in 2012, his company was approaching the one-year mark in a clinical trial of eteplirsen.

DMD, a genetic disorder that targets boys, is usually diagnosed around kindergarten. It saps muscle strength and by adolescence leaves many of its victims in wheelchairs. Boys with DMD lack the protein dystrophin, which is critical to muscle function. In time, their hearts and respiratory systems stop working. Few survive past their 20s.

Researchers believed eteplirsen could help patients produce enough of the missing protein to slow DMD’s progression.

“This drug works,” Ms. McNary said, introducing herself to Mr. Garabedian at the DMD conference. Her youngest son, Max, 10 years old at the time, was one of a dozen boys enrolled in the eteplirsen drug trial at the Nationwide Children’s Hospital in Columbus, Ohio. After four months on the drug, she said, Max could open a milk carton and needed a wheelchair less often.

Ms. McNary turned out be the cheerleader Mr. Garabedian needed. His company had just been warned by the Nasdaq Stock Market that its share listing might be dropped from the exchange for trading below $1.

Mr. Garabedian told the Journal his company was having trouble raising money after it had spent $30 million on eteplirsen in the 18 months since he had joined as CEO.

Doses of the drug eteplirsen to treat Duchenne muscular dystrophy. Photo: Adam Glanzman for The Wall Street Journal

Before eteplirsen would be available to the 1,000 or more sick boys who might benefit in the U.S.—and before the company could charge patients more than $300,000 a year for the treatment—the drug needed FDA approval.

Looking back, Catherine Collins, whose son has DMD, said: “Sarepta used the parents to push their regulatory agenda. We were willing participants, but they were trading on our desperation.”

Edward Kaye, Sarepta’s chief executive since 2015, said the company was “able to make a true partnership” with DMD patient groups, helping parents give the FDA firsthand observations of how the drug had worked for their sons.

Former FDA Commissioner Robert Califf, who stepped down in January, said the Sarepta case was “an example where things should have been done better…There should be disclosure of the source of documents and presentations, and who was involved.”

Hopeful shortcut

Mr. Garabedian and Dr. Kaye, the company’s chief medical officer at the time, revealed at the 2012 conference early data from the drug trial that suggested eteplirsen was working.

With the stock trading below $1, Mr. Garabedian didn’t have the luxury of waiting to spread encouraging news. Trial researchers were measuring levels of the protein dystrophin in the patients, all boys, and how far they could walk in six minutes.

Dr. Kaye said it appeared the drug helped lift dystrophin levels. Even better, 10 of the 12 boys in the trial walked, on average, more than 50 feet farther during the timed walk, he said; two boys became unable to walk.

Two weeks after the conference, the company made a 1-for-6 stock split, which raised its share price and allowed it to keep its Nasdaq listing. It also changed its name to Sarepta from AVI BioPharma Inc.

Oct. 3, 2012 Sarepta shares reach nearly $45 after the company issues positive drug trial results.

Oct. 3, 2012 Sarepta shares reach nearly $45 after the company issues positive drug trial results.

The company in a July 24 news release said the boys showed “significant clinical benefit” after 36 weeks of treatment. Shares jumped past $8. Another positive news release at the 48-week mark pushed the stock close to $45.

Even with the promising news, Mr. Garabedian’s company had concerns about whether it could raise enough money to support third- and fourth-phase drug trials, which must show drugs work effectively and safely. Parents, meanwhile, were clamoring for a treatment.

One shortcut was accelerated approval—that’s when the FDA gives permission to dispense a drug before proving a clinical benefit. It allows patients a quicker chance at treatment for maladies that have none, such as DMD. Sarepta’s application would rely on trial data showing that eteplirsen would be “reasonably likely” to produce a clinical benefit, rather than proving it was effective.

That fall, Mr. Garabedian met Christine McSherry, a former nurse of Pembroke, Mass., whose son, Jett, now 21, had been diagnosed with DMD on his fifth birthday. Ms. McSherry said she was so upset at the news she briefly considered killing herself and her son. Instead, she became an advocate for treatment. She began speaking regularly with Mr. Garabedian and other Sarepta managers to learn about the FDA’s regulatory machinery.