The Thalys station in the northern city of Lille has also started using them, Pepy told French television.
The decision to install airport-style security gates was prompted by the November 13 Paris attacks that claimed 130 lives.
There was also a failed attack in August on a Thalys train linking Amsterdam and Paris.
"We think that since France is a pioneer on the Thalys, other countries will think about it themselves and probably take the same decision," Pepy said.
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"The metal detectors are not a panacea... I don't believe in a miracle solution. Today we have three security nets: human presence, new technology, and everyone's vigilance."
Pepy said that the idea of "conducting patrols in the trains, armed and in plainclothes" was under consideration, as well as a "sniffer machine for suspect packages."
SNCF's annual security budget is 500 million euros (USD 545 million), he added.
"It's done in the aviation industry," he said.