Myanmar has been riven by violence and turmoil after its military toppled Aung San Suu Kyi's government in a coup over two years ago.
China is a major ally and arms supplier of the internationally isolated junta and has refused to condemn the putsch.
Beijing also backs and arms several ethnic rebel groups along its border with Myanmar, analysts say.
Some of these groups have clashed repeatedly with the military in the aftermath of the coup, and an alliance of China-backed rebels in March called for Beijing's help to defuse the crisis.
China appointed a special envoy to Myanmar, Deng Xijun, in December, who has met junta chief Min Aung Hlaing at least twice since and has also met ethnic rebel leaders.
Qin visited the China-Myanmar border on Tuesday, calling for "friendship and cooperation" between the two countries.
Several projects in Beijing's Belt and Road Initiative are slated to run through northern Myanmar and link China's landlocked Yunnan province with the Indian Ocean.
Qin's predecessor, Wang Yi, visited the country in July last year, meeting with his local counterpart but not with the junta chief.
After his Myanmar visit, Qin will travel to India for a meeting of Shanghai Cooperation Council (SCO) foreign ministers, the Chinese foreign ministry said, without providing further details about his itinerary.
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