Weimer begins his new role in January, and will take over from Carsten Kengeter, who will leave Deutsche Boerse at the end of 2017.
At UniCredit, Weimer has been spokesman of the management board of HypoVereinsbank at UniCredit Bank AG since 2009.
Weimer joined the bank in 2007 as UniCredit Group’s head of global investment banking, based in Munich.
Weimer said: "I am looking forward to a challenging task in a very international and technologically leading global company whose roots lie in Frankfurt as a financial centre. In a financial centre that should become even stronger. Deutsche Börse will make its contribution to achieve this.”
The appointment was confirmed at the supervisory board of Deutsche Boerse AG’s meeting earlier today.
Joachim Faber, chairman of the board, said: "Theodor Weimer has strong leadership skills and possesses many years of capital market experience–I am very pleased that he will take over the CEO role.”
“Theodor Weimer is a highly respected financial sector expert who understands the business of our clients very well. He is both internationally oriented and deeply rooted in our home market, and very well connected with regulators. He has all the prerequisites to successfully continue Deutsche Börse Group's growth agenda."
Alongside Weimer’s appointment, the board also extended the contracts of Andreas Preuss as deputy CEO and Jeffrey Tessler as head of Eurex and Clearstream.
Preuss is responsible for IT, operations, the data business and the subsidiaries EEX and 360T.
Tessler is responsible for clients, products and core markets of Deutsche Boerse’s highest earning business segments.
Kengeter announced last month that is stepping down as CEO amid an ongoing investigation into insider trading activity. At the time, Deutsche Boerse said he had taken the decision to allow the firm to focus on business, clients and growth, and to avoid further burdens caused by the ongoing investigation.
Faber said: "On behalf of the entire supervisory board, I would like to thank Carsten Kengeter, who established strong new strategic direction for the company in a difficult time and enhanced the company's competitiveness."
He added: "By appointing Theodor Weimer and extending the contracts of Andreas Preuss and Jeffrey Tessler, it is possible to give the company new impetus on the one hand and ensure the necessary continuity in the work of the executive board on the other hand."