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SAN FRANCISCO — Wells Fargo & Co. said Thursday it has agreed to handle the credit card business of online payment provider PayPal Inc., which has struggled to stay in good graces with both the Mastercard and Visa payment systems. 

San Francisco-based Wells will replace Electronic Payment Exchange Inc., which took over from Chase Merchant Services late last year. Wells is supposed to take over the job by November and continue processing PayPal’s credit card transactions until May 2004, according to Securities and Exchange Commission documents. 

The alliance is designed to rid Mountain View-based PayPal of a major headache — dealing with the rules and regulations of Mastercard and Visa. 

“This was a natural fit,” said Debra Rossi, a Wells executive vice president. “We can handle the credit card regulations and PayPal can focus on growing its business.”