A director of Al-Haramain Foundation, Sulayman al-Buthi, was placed on the UN list of terrorism financiers and accused of having links to al-Qaida and Usama bin Ladin.
In his letter, al-Buthi warned against the perception in the US that Saudi charities were being used to fund terrorism.
"The common United States practice of freezing charities and charitable organisation officials' bank accounts based upon 'secret evidence' only serves to reinforce the image the United States simply wants to end faith-based giving rather than truly rooting out the evils of terror finance," he said in the letter dated 2 February.
Giving money to charity, known in Arabic as zakat, is a tenet of Islam.
Al-Haramain Foundation is one of six Islamic charities in the US that have been closed by authorities since the 11 September 2001 attacks.
No charge has ever been brought against al-Buthi in a court of law.
A US senator called US policy in
Saudi Arabia a success so far
Senator George Allen responded to al-Buthi by saying that US policy in Saudi Arabia had so far been successful.
"These conjoined efforts have proven to be successful. As you know, with the aid of US officials, Saudi law-enforcement agents have apprehended and/or killed a number of terrorists," Allen wrote in a letter.
But Allen did not address any of the unproven and unpublicised accusations against the Saudi or his charitable work.
Al-Buthi said that he was pleased his letter had been read by the senator.
"I think it's good," he said referring to Allen's response. "For me I was happy for a member of congress just to read it."
Describing himself as one of the "big critics" of groups such as al-Qaida, al-Buthi said he hoped the letter would be the start of a new exchange between the two countries.
"The relations between the US and Saudi Arabia have been twisted in another direction," he said. "We would like to open a dialogue. We don't want to open a clash."
Al-Buthi also questioned the rationale of the US government's pressure on Islamic charities, and argued that Washington would be in a better position to investigate security concerns if there was coordination between the directors of such charities and US officials.