The "Prey" and the "Kidd" series are the only two John Sandford book series that were written and should be read in chronological order. Fans can read the "Singular Menace" and "Virgil Flower" series in any order they choose.
As of 2015, there are 25 published books in the "Prey" series starting with "Rules of Prey" and ending with "Gathering Prey." A full list of the titles along with the order they are intended to be read in is available on the FAQ page of JohnSandford.org. The author's website also acknowledges that while this series is intended to be read in a specific order, many readers don't read them that way.
The "Kidd" series contains four titles as of 2015, and they should be read with "The Fool's Run" first, followed by "The Empress File," "The Devil's Code" and finally "The Hanged Man's Song." While this series was also written in a specific order, the paperback version of the second novel, "The Empress File," erroneously names it as the first in the series, leading many readers to read that series out of order as well. The author does not plan on adding any additional titles to this series, although he has not completely ruled it out.