President Going to Germany
Pahor's visit comes just over a week after he was in Paris for talks with senior officials there.
Both tours of EU capitals are a part of efforts to strengthen bilateral relations, discuss the future of the EU and present Slovenia's plans to balance public finances and kick-start economic recovery, Pahor's office has said.
The office of the German president told the STA the agenda would include bilateral and international issues.
The office of Chancellor Merkel said on its website the talks would be dominated by bilateral issues, EU topics as well as the situation in Slovenia and the region.
The last high-level talks between the two countries were held in May 2012, when Janez Janša visited Germany in what was his first foreign visit after becoming prime minister.
In August 2011, Merkel paid a visit to Slovenia and the two countries signed a declaration on enhanced cooperation.
Slovenia and Germany have a long history of close relations, political as well as economic.
Germany is a key trading partner, accounting for a fifth of Slovenia's exports, and its companies are among the biggest foreign investors in Slovenia.