Shen was back to the spotlight of Chinese football when he joined Beijing Guoan and served under Jin Zhiyang as an assistant coach in 1997. Shen took over most of the coaching in the middle of the season, since Jin was summoned to the China national football team to assist Qi Wusheng. In 1998, Shen was named the head coach of Beijing Guoan and Jin left the club to assist the newly installed head coach of the China national football team Bobby Houghton. Shen was able to lead the club to finish third in the 1998 Jia A, but the next year Beijing Guoan showed a poorer quality and finished sixth in the league. The result was the worst one for the club since 1995. Shen was replaced at the end of the season.