Beijing has invested billions of dollars in building rail and road routes that traverse Central Asia, long seen by Russia as its sphere of influence.
Wearing a traditional felt hat, Japarov spoke at a ceremony shown live on Kyrgyz state television, which included the launch of flares in the three countries' national colours in the snowy mountains of the Jalal-Abad region in the south of the Central Asian country.
Covering a distance of almost 523 kilometres (325 miles), the strategically important railway will run west from the Chinese city of Kashgar in the northwestern Xinjiang region through the Kyrgyz border city of Jalal-Abad to Andijan in Uzbekistan.
The section in China will be around 155 kilometres while the Kyrgyz section will be the longest at 305 km and the Uzbek section will be 63 km.
"This route will ensure supply of goods from China to Kyrgyzstan and then onto Central Asia" and nearby countries "including Turkey" and "even to the European Union", Japarov said at the ceremony.
He thanked "our partners -- China and Uzbekistan -- for assistance in carrying out this project".
The project, which Kyrgyz authorities estimate could cost up to $8 billion, includes the construction of railways in mountainous areas and in areas of permafrost, where the ground never fully thaws.
In Kyrgyzstan, it calls for the construction of 27 tunnels and 46 bridges, the televised presentation said.
Construction will be "very complex", it added, taking place in a mountainous area with a harsh climate and high seismic activity.
The project had been under discussion for two decades but was finalised in June when the leaders of China, Kyrgyzstan and Uzbekistan signed an intergovernmental agreement.
Kyrgyz Railways said it could take about six years to build.
China is building ties with Central Asia, a region rich in hydrocarbons and a vital link in its colossal Belt and Road infrastructure project aimed at expanding its clout overseas.
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