"Everton FC can forget about coming up with an offer," Dortmund chairman Hans-Joachim Watzke told Bild.
"We do not think about selling Neven, he is a key part of our future plans."
Subotic joined Dortmund from Mainz last summer and is contracted to the Bundesliga club until June 2013.
He admits he would consider a move to a different league at some point in the future, but not at this stage of his career.
"I am under contract at Borussia Dortmund and I am feeling well being there," said Subotic. "Mid-term it could become an option to move abroad, but at this period of time a move to another country would be much too early for me.
"I feel there is something good going on at Borussia Dortmund, our team can do a lot next term and I like being part of this."