Thompson, who wrote the book Fear And Loathing In Las Vegas, died on February 20, 2005 at the age of 67 in his home in Woody Creek, Colorado from a gunshot wound to the head.
The Colorado Bureau of Investigation said the case review is being conducted at the request of his widow, Anita Thompson.
Sheriff Michael Buglione said: "We understand the profound impact Hunter S Thompson had on this community and beyond.
"By bringing in an outside agency for a fresh look, we hope to provide a definitive and transparent review that may offer peace of mind to his family and the public."
Officials said the review process is expected to take "an unspecified amount of time" and added that "there is no firm deadline for its completion".
Thompson's semi-autobiographical story about the counterculture of the 1960s was adapted into a film starring Johnny Depp in 1998.
Besides the 1970s drug haze classic, the journalist was also credited with pioneering New Journalism - or "gonzo journalism" - in which the writer made himself an essential component of the story.
His other books included Hell's Angels, Generation Of Swine and The Rum Diary, which was adapted into a movie starring Depp in 2011.
At his memorial in Colorado, part-financed by Depp and hosted by his widow, Thompson's ashes were shot out of a canon, as per his final wishes.
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