"Protections that promote equality and diversity should not be conditional on someone's sexual orientation," he wrote in the op-ed, which was published online Sunday. "For too long, too many people have had to hide that part of their identity in the workplace."
Cook, who is gay, argued that respecting people's individuality is a civil rights issue and is good for business.
Cook urged Congress to "strike a blow" against intolerance by passing the Employment Nondiscrimination Act.
"So long as the law remains silent on the workplace rights of gay and lesbian Americans, we as a nation are effectively consenting to discrimination against them," he wrote.
Federal law prohibits discrimination based on race, sex, religion, age and disability but there are no federal protections for sexual orientation or gender identity.
Apple has gotten involved in other gay rights issues, such as donating to the campaign against California's Proposition 8, which banned same-sex marriage. Apple, along with hundreds of other companies, also filed a brief with the Supreme Court opposing the Defense of Marriage Act.
The Employment Non-Discrimination Act has the support of every Democrat in the Senate and a handful of Republicans. But it faces longer odds in the Republican-controlled House.
President Obama urged Congress to enact the bill in his own op-ed in the Huffington Post on Sunday.