Li met with Swiss officials in Zurich on Friday to conclude three years of negotiations.
In an op-ed published Thursday by Swiss newspaper Neue Zuercher Zeitung, Li said the deal showed China was committed to free trade.
Trade between the two nations topped $26 billion last year.
Switzerland is the first European stop on Li's inaugural trip abroad since taking office in March. He travels to Germany on Saturday for talks with Chancellor Angela Merkel.
Concerns have grown recently about a possible trade war between China and the European Union over solar energy products.
Switzerland isn't an EU member.
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