[7][8] During Vardarajan's tenure as the editor, Bharatiya Janata Party (BJP) leader Subramanian Swamy filed a case in Delhi's High Court challenging his appointment as editor on the grounds that Varadarajan was not an Indian citizen, and further complained to the Ministry of Information and Broadcasting, Government of India.

[16][17] He has also served as a senior fellow at the Center for Public Affairs and Critical Theory at Shiv Nadar University in Delhi.

[23] In November 2005, the United Nations Correspondents Association awarded Varadarajan the Elizabeth Neuffer Memorial Prize Silver Medal for Print Journalism for a series of articles, Persian Puzzle on Iran and the International Atomic Energy Agency.

[24] In March 2006, he was awarded the Bernardo O'Higgins Order by the President of Chile—that country's highest civilian honor for a foreign citizen—for his contributions to journalism and to the promotion of India's relations with Latin America and Chile.

[26] He received the 2017 Shorenstein Journalism Award for outstanding reporting and for significant contributions to promoting freedom of the press in the Asia-Pacific region.

[31] On 31 March 2020, The Wire had published a news report on a Ram Navami fair being conducted amidst the coronavirus pandemic in Uttar Pradesh.

On the following day, the report was corrected and Varadarajan himself issued a clarification, attributing the quote to the Hindutva stalwart Acharya Paramhans.

[32] The Uttar Pradesh police registered a case against Varadarajan calling it an "objectionable article" and on a number of charges including promoting enmity, cheating by impersonation and creating false alarm leading to panic.

[37] The police at Rampur, Uttar Pradesh registered an FIR against Varadarajan on charges of public mischief and imputations against national integrity for publishing and tweeting the report.

[36] FIRs on similar grounds were also lodged against six other journalists including Vinod Jose of The Caravan which had reported on eyewitness claims that the police had shot the farmer and against the member of parliament Shashi Tharoor.