Even after splitting up later this year, eBay Inc. and payments unit PayPal will be joined at the hip.

EBay has agreed to ensure that roughly 80% of gross merchandise sales on its online marketplace are routed through PayPal for the next five years, as they are today. If PayPal's share dips below that level, eBay will have to pay its former subsidiary restitution.

For its part, PayPal has agreed to pay eBay a commission if its percentage of sales on the marketplace rise above that mark.

The payment arrangement is among the details that emerged Thursday in a securities filing from eBay as it prepares to cleave off PayPal in the second half of the year. The filing didn't offer any additional details on the split's possible timing.

The operating agreement will preserve for six years, including a one-year transition period, a relationship much as it was before the split.

EBay Chief Executive John Donahoe, who will leave his post and become chairman of PayPal, said the accord is designed to give both firms flexibility. For example, he said either company can negotiate joint ventures with other firms without approval from its former partner.

"PayPal is free to pursue any merchant, to pursue an Amazon, an Alibaba, " said Mr. Donahoe in an interview. "And eBay is free to bring other payment alternatives onto eBay."

Under pressure from activist investor Carl Icahn, eBay last year said it would spin off PayPal to create two independent, publicly traded companies. EBay's separation plan will require approval from the U.S. Securities and Exchange Commission, which Mr. Donahoe said he expected.

The agreement forbids eBay from creating its own payments system, and PayPal from developing a marketplace for selling merchandise.

EBay Chief Financial Officer Bob Swan also will step down after the split, though he'll join the eBay board. EBay founder Pierre Omidyar will have a board seat on both companies. EBay director Tom Tierney, a former Bain & Co. CEO, is set to become chairman.

The 54-year-old Mr. Donahoe, also a former Bain & Co. executive, said he had not determined what he would do after he steps down as CEO.

EBay generates more profit, but it is growing more slowly than PayPal and faces continued threats from e-commerce giants Amazon.com Inc. and Alibaba Group Holding Ltd. It also will have to overcome a continuing problem with Google Inc.'s search algorithm that pushes Web-users to other sites.

Meanwhile, PayPal has been on a pace to overtake the eBay marketplace unit by sales and with more than 160 million active accounts, has a considerable lead over upstarts like Square Inc.

EBay is cutting about 2,400 jobs this year in anticipation of the split and announced a plan to seek a buyer for eBay Enterprise unit, which helps other companies with their online sales efforts.

Write to Greg Bensinger at greg.bensinger@wsj.com

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