The private correspondence between the pair, who were close friends, revealed that Lady Thatcher thought of the EU as 'contrary to British interests and damaging to our Parliamentary democracy'.
Sir Bill, who has been the MP for Stone since 1997 having previously been the MP for Stafford from 1984, said that Lady Thatcher had given him instructions to release the letter if there was ever a time when it was called into question where she would have signed up to the European project.
The release of the letter comes after Lady Thatcher's private secretary during much of her time in Downing Street, Charles Powell, claimed she would have backed David Cameron's renegotiation and voted to stay in the EU.
Her letter to Sir Bill was sent in 1993, shortly after the EU was established under its current name following the Maastricht Treaty.
By this point, Lady Thatcher had stepped down as an MP and was thus unable to vote on the proposal.
However in her letter she wrote: "I understand it is being suggested in some quarters that I would have agreed to the Maastricht Treaty. May I make it clear that I would NOT have done so. In my view it is contrary to British interests and damaging to our Parliamentary Democracy."
He added: "She gave the letter to me for a specific purpose and she had trust in me that I would do what she wanted.
"I am now doing that. There has never been the same degree of necessity to (release it) as there is now."
Sir Bill said her comments on Maastricht should leave no-one in any doubt that she would wish to leave the EU the Treaty had gone on to create.
Sir Bill and his family enjoyed holidays with Lady Thatcher and her family.