In March 2013, Rajnath Singh appointed Varun Gandhi as the national general secretary of the BJP. He became the youngest ever general secretary of the party. In May 2013, Varun Gandhi was made in charge of the BJP's affairs in West Bengal. In June 2013, Gandhi requested Lok Sabha Speaker Meira Kumar to call an emergency all party meeting in view of the calamity in Uttarakhand in which thousands of people had died. He suggested a number of step like contribution from MPLADs fund, forgoing of three months' salary by MPs and tax incentives for corporate and individuals for help. He has said that he spoke to many MPs and all of them were ready to contribute. He said that the Speaker should act as a catalyst and coordinate the action plan.
In July 2013, Gandhi handed over a cheque of Rs 1 lakh from his salary account to family members of former Jan Sangh Member of Legislative Assembly late Bhagwati Prasad, who died at a government hospital after prolonged illness and age-related complications. The former MLA had to spend over an hour on the floor of an emergency ward before doctors at the hospital realised he was an ex-MLA and was subsequently given medical attention. His family didn't even have money to perform the last rites after his death. Varun said he came to know about Prasad only after his death. Describing the late MLA as a model of honesty, he said it was hard to find an honest leader like him.
In August 2013, newspapers reported that Gandhi was the only MP in the country who had spent all of his MP Local Area Development Fund (MPLAD) before stipulated time. According to official sources, Varun Gandhi used his funds for the development in education, health and infrastructure activities. His proposals were worth more than the entire MPLAD fund thus ensuring the entire amount of 25 crore was spent during his tenure as a Member of Parliament. His political aides stated that he submitted the proposals on time and also employed his personal team to monitor the use of money.
In September 2013, Varun Gandhi accused the Samajwadi Party-led Uttar Pradesh government of pursuing the politics of appeasement, and said that its mistakes would lead to its collapse, after it denied permission to Varun Gandhi's rally in Agra just two days before it was scheduled to take place.