U.S. District Judge Edward Davila in San Jose, California, imposed the sentence on Balwani, who was convicted by a jury on two counts of conspiracy and 10 counts of fraud in July.
Prosecutors said Balwani, 57, conspired with Holmes, 38, to deceive Silicon Valley investors into believing the company had achieved miniaturized machines that could accurately run a broad array of medical diagnostic tests from a small amount of blood.
Meanwhile, the company secretly relied on traditional methods to run tests and provided patients with inaccurate results, prosecutors said.
Holmes, who started the company as a college student and became its public face, was indicted alongside Balwani, her former romantic partner, in 2018.
Davila later granted each a separate trial after Holmes said she would take the stand and testify that Balwani was abusive in their relationship. He has denied the allegations.
Holmes was convicted in January on four counts of fraud and conspiracy but acquitted of defrauding patients.
Davila sentenced Holmes to 11-1/4 years in prison at a hearing last month, calling Theranos a venture "dashed by untruths, misrepresentations, plain hubris and lies."
Prosecutors subsequently argued Balwani should receive 15 years in prison, saying he knew Theranos' tests were inaccurate from overseeing the company's laboratory operations, and decided to "prioritize Theranos' financial health over patients' real health."
The probation office had recommended a nine-year sentence.
Balwani's attorneys asked for a sentence of probation, arguing that he sought to make the world a better place through Theranos and was not motivated by fame or greed.
Once valued at $9 billion, Theranos promised to revolutionize how patients receive diagnoses by replacing traditional labs with small machines envisioned for use in homes, drugstores and even on the battlefield.
The company collapsed after a series of Wall Street Journal articles in 2015 questioned its technology.
The case is U.S. v. Balwani, U.S. District Court, Northern District of California, No. 18-cr-00258.
(Reporting by Jody Godoy in New York; Editing by Noeleen Walder and Bill Berkrot)
By Jody Godoy