Upon graduation from high school in 1997, he chose to play college baseball at Yonsei University instead of turning pro directly.

In July 1997, as a freshman Shin was selected to play for South Korea in the 8th Korea–USA College Baseball Championship Series.

In April 1998, Yonsei University captured the 32nd President's Flag College Championship, and Shin dominated the competition by winning the batting and stolen base titles and earning the MVP honors.

Shin spent much of the summer of 1998 overseas with the South Korean national team, taking part in a tour of Japan and United States and competing in the Baseball World Cup held in Italy.

In December 1998, he was selected for the South Korea national team again that finished in 1st place at the 1998 Asian Games in Bangkok, Thailand.