When Qatar’s royal family was looking for advice on charitable giving, it turned to a well-regarded professor named Abd al-Rahman al-Nu’aymi. The 59-year-old educator had a stellar résumé that included extensive fundraising experience and years of work with international human rights groups.

But one apparent accomplishment was omitted from the list: According to U.S. officials, Nu’aymi also was working secretly as a financier for al-Qaeda, funneling millions of dollars to the terrorist group’s affiliates in Syria and Iraq even as he led campaigns in Europe for greater freedoms for Muslims.

Nu’aymi was one of two men identified by Treasury Department officials last week as major financial backers of al-Qaeda and its regional chapters across the Middle East. Although U.S. officials routinely announce steps to disrupt terrorist financing networks, the individuals named in the latest case are far from ordinary. Both men have served as advisers to government-backed foundations in Qatar and have held high-profile positions with international human rights groups. The second man, a Yemeni, is heavily involved in his country’s U.S.-backed political transition.

Their alleged dual roles — promoting humanitarian causes and civil rights while simultaneously supporting extremist groups — reflect a growing challenge for counterterrorism officials attempting to monitor the torrents of cash flowing to Islamist rebel groups in Syria, current and former U.S. officials say.

“Individuals with one foot in the legitimate world and another in the realm of terrorist financing provide al-Qaeda with a cloak of legitimacy,” said Juan Zarate, a former Treasury Department official and author of “Treasury’s Wars,” a book that describes U.S. efforts to penetrate terrorist financial networks. Zarate said such cases greatly complicate the “financial diplomacy” involved in attempting to disrupt terrorist support networks, especially private funding from wealthy Persian Gulf donors seeking to help Syria’s rebels.

Despite attempts by gulf states to crack down on jihadist financial networks, former and current U.S. officials have described a surge in private support for Islamist extremists in Syria, particularly in Qatar and Kuwait.

The Obama administration has repeatedly urged both countries to rein in private donations to jihadists, while acknowledging that new tactics, including the widespread use of Twitter and other social media, make fundraising more difficult to track.

“It is essential for countries to take proactive steps to disrupt terrorist financing, especially where al-Qaeda and its affiliates are concerned,” David S. Cohen, the Treasury Department’s undersecretary for terrorism and financial intelligence, said in announcing financial restrictions against Nu’aymi and the Yemeni national, Abd al-Wahhab al-Humayqani. Cohen said the Obama administration would continue to work with the gulf region’s capitals to “ensure that charitable donations are not used to support violence.”

The administration’s action last week named both men as “specially designated global terrorists,” a determination that allows U.S. officials to freeze their financial assets and bar American citizens and companies from doing business with them. Treasury Department documents alleged that both men used their charity work to conceal efforts to raise millions of dollars for al-Qaeda and other terrorist groups, from Syria to the Horn of Africa.

The naming of the two officials raised eyebrows in Qatar and Yemen, where supporters viewed the allegations as politically motivated. Both men have been prominent critics of U.S. counter­terrorism policies, particularly the use of drone strikes against terrorism suspects.

Nu’aymi, a Qatar University professor and former president of the Qatar Football Association, was a founding member of a prominent charity — the Sheik Eid bin Mohammad al-Thani Charitable Foundation, named for a member of the country’s ruling family. In recent years, Nu’aymi had gained renown as an international activist, serving as president of Alkarama, a Geneva-based human rights organization that works closely with the United Nations and major international activist groups to advocate for Muslims’ civil rights.

Alkarama lobbies on behalf of Islamist detainees around the world, and it accuses Western and Arab governments of suppressing the rights of political groups that promote Islamic rule for the Middle East. Recently, the group has spoken out against U.S. drone strikes. Some of the group’s former clients are linked to Islamist militias seeking to overthrow Syrian President Bashar al-Assad.

Humayqani is an Alkarama founding member and onetime adviser to Qatar on charitable giving, according to his résumé. He is a founding member of Yemen’s conservative Rashad Union party and has served on the country’s National Dialogue Conference, a group established in the wake of the Arab Spring uprising to advise the government on political and economic reforms. The U.S. government strongly backs the National Dialogue with political and financial support.

Nu’aymi, in a response posted on Twitter last week, said the U.S. allegations were in retaliation for his criticism of American policies, including drone strikes in Yemen and U.S. support for the recent overthrow of Egypt’s democratically elected government. He said the U.S. claims about his fundraising work were “far from the truth.”

Humayqani was traveling and could not be reached for comment. A statement released by his Rashad Union party condemned what it called “false accusations” by the United States and urged Yemen’s government to rally to his defense.

The allegations against Nu’aymi come at a time of increasing U.S. concern about the role of Qatari individuals and charities in supporting extreme elements within Syria’s rebel alliance. One charity, Madid Ahl al-Sham, was cited by Jabhat al-Nusra in August as one of the preferred conduits for donations intended for the group, which has pledged loyalty to al-Qaeda leader Ayman al-Zawahiri.

Root reported from Sanaa, Yemen.