The meeting between Jaishankar and McMaster assumes significance as the top military leader was appointed as the National Security Advisor by US President Donald Trump ten days ago.
During the meeting held at the White House, the two officials are believed to have discussed issues related to security, counter-terrorism and defence partnership.
Jaishankar also met Speaker of the House of Representatives Paul Ryan and discussed various issues, including ways to enhance economic and defence cooperation between the two countries.
"We had a great opportunity today to build on this critical partnership by discussing ways to enhance our economic and defence cooperation," he said.
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During his meeting with Jaishankar, Ryan expressed condolences of the US House of Representatives over the death of Indian techie Srinivas Kuchibhotla.
"Our peoples must continue to stand together, and I look forward to working with Foreign Secretary Jaishankar in the years ahead," Ryan said.
Kuchibhotla, 32, was killed and another Indian Alok Madasani injured by navy veteran Adam Purinton, who yelled "terrorist" and "get out of my country" before firing on him.
This is his third-trip to the US after Trump was elected as the President.
Trump had pledged to strengthen the Indo-US ties during his telephonic conversation with Prime Minister Narendra Modi last month.
About three weeks before his electoral victory, Trump had told Indian-Americans that he would be India's best friend at the White House.
Jaishankar, during his visit, is likely to discuss with top US officials India's concerns over a possible clamp down on H-1B visas and safety of Indians.