Media speculation in Italy has claimed the Dutchman is a target of Thohir with the Indonesian businessman looking at possible candidates to replace current coach Walter Mazzarri.
However, Thohir said on www.inter.it: "He (De Boer) is a good coach but there are no negotiations open with him.
"I don't know him and I have never met him."
Inter have endured a difficult campaign under Mazzarri, who replaced Andrea Stramaccioni at the end of last season.
The Nerazzurri are fifth in Serie A, 28 points adrift of league leaders Juventus.
Mazzarri is under contract with Inter until June 2015.