The 28-year-old finished with a time of 37.92 seconds, just 0.18 seconds behind home favourite Yukino Yoshida in the opening event of the World Cup season.
South Korea's Min-Sun Kim claimed third place with a time of 37.93.
The three-day opening World Cup leg in Nagano runs until Sunday.
In February, Wójcik, alongside teammates Iga Wojtasik and Karolina Bosiek, won bronze in the women's team sprint at the long-track speed skating world championships in Calgary, Canada.
Earlier that month, the Polish team finished runners-up in the same event at the World Cup in Quebec City.
In December last year, Wójcik captured an individual World Cup bronze in the women's 500 metres on home ice at the Tomaszów Mazowiecki Ice Arena in central Poland.
In December 2021, she triumphed in the women’s 500 metres at the World Cup in Salt Lake City, becoming the first Polish female speed skater to win a World Cup event since Erwina Ryś-Ferens in 1988.
Andżelika Wójcik skates to victory in the women's 500 metres at the speed skating World Cup in Salt Lake City on December 4, 2021. Photo: EPA/GEORGE FREY
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Source: IAR, PAP, eurosport.tvn24.pl