Other names joining the list include Limmy, Irvine Welsh, Ian Rankin and Dr Brooke Magnanti.
The trust has compiled the rundown ahead of next week's Book Week Scotland, which will see more than 450 events taking place across Scotland.
The country's top wordsmith tweeters were picked for followers, interaction and their "social authority" ranking.
Here's a look at the Top 10 writers in Scotland on Twitter, in their own words:
1. JK Rowling - author of the world conquering Harry Potter series.
2. Limmy - comedian, author and gamer.
3. Irvine Welsh - pioneering author of Trainspotting, Filth and Porno.
4. Ian Rankin - Rebus creator and Scottish crime king.
5. Dr Brooke Magnanti - author, forensic scientist and Belle de Jour blogger.
6. Neil Mackay - journalist, novelist, radio broadcaster.
7. Mark Millar - comic book supremo and 20th Century Fox creative consultant.
8. John Niven - A&R survivor, author and screenwriter.
9. Alan Bissett - novelist, playwright and performer.
10. Estelle Maskame - teenage author of Did I Mention I Love You? trilogy
Danny Scott, social media manager at the Scottish Book Trust, said: "People may be surprised to see authors with huge followings ranked lower than authors with more modest numbers.
"But, as this research proves, regular engagement is everything on social media. The authors at the top of this list all interact with their audience and aren't afraid to offer an opinion, or, indeed, be themselves.
"In many ways, the research proves that authors are becoming as much of a commodity as their novels."
JK Rowling has headed up a list of top writers on Twitter put together by the Scottish Book Trust.