Braintree's payments technology is used by popular startups such as vacation rentals site Airbnb, cab-hailing app Uber and restaurant reservations site OpenTable.
The move comes as eBay's PayPal unit works to evolve from its roots as an online payments provider, expanding its offline, mobile and online offerings to stores, restaurants and other business.
San Jose, Calif.-based eBay Inc. says that it will operate Braintree as a separate business. Bill Ready, the CEO of the Chicago-based company, will report to PayPal President David Marcus.
Braintree's roughly 200 employees are staying with the Chicago-based company.
EBay says it expects to close the deal before the end of the year.
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