He was the varsity baseball coach at Westminster Christian Academy for 33 years, compiling a record of 537 wins and 283 losses. Westminster won the Missouri High School State Championship four years in a row from 2011 to 2014. The team made the Final Four in 2006, 2007 and 2017. Van Gilst won ten conference championships and ten district championships. Westminster won the Metro League championship every year from 2012 to 2017, only losing one game in league play during those six years. Westminster also won the district championship every year from 2006 to 2014, and then again in 2017.

Westminster won the Missouri State Championship in 2011, 2012, 2013, and 2014. Each year, Van Gilst was named Coach of the Year by the Missouri High School Baseball Coaches Association. In 2012, he was named Missouri State Coach of the Year by the Missouri Coaches Association. He was also voted Coach of the Year by the Missouri State High School Activities Association, and the National Federation of High Schools chose him as Coach of the Year for Missouri. The National High School Baseball Coaches Association selected Van Gilst as the Midwest Region Coach of the Year in 2012 and 2014. He was the Max Preps National Coach of the Year in 2014. In 2006 and 2016, he received the Hal Whitaker Coach of the Year Award presented by the Greater St. Louis Association of Umpires.

In 2013, Van Gilst was inducted into the Missouri High School Baseball Coaches Association Hall of Fame. In 2017, he was inducted into the Greater St. Louis Amateur Baseball Hall of Fame. Van Gilst was a member of the Missouri High School Baseball Coaches Association for many years.

Before coming to Westminster, he was an assistant varsity baseball coach for five years at Timothy Christian High School in Elmhurst, Illinois. He was head varsity baseball coach for seven years at Fort Lauderdale Christian High School in Fort Lauderdale, Florida.