The deal, which also covers finance, accounting and human resources could be worth £200m, if service level agreements are met.
This contract supersedes an agreement the two companies signed in early 2002 and was necessary following Thomas Cook's merger and integration of MyTravel functions in June.
Thomas Cook's operational back-office systems include a SAP-based enterprise resource planning system. Additionally, network management and technical services finance and accounting services, and HR services will be delivered by Accenture through its UK shared services centre.
"The relationship has and will continue to support our delivery of back office [operations]," said Manny Fontenla-Novoa, joint chief executive of Thomas Cook Group.