In 1999, he was instrumental in the BJP's withdrawal of support to Bansi Lal's Haryana Vikas Party, and backing Om Prakash Chautala instead.
The BJP withdrew support to Bansi Lal government amid reports of an imminent merger of the Haryana Vikas Party with the Congress.
In 2004, Khattar got charge of 12 states, including Delhi and Rajasthan. He worked with veteran RSS ideologue Bal Apte, who was then heading the Chunaav Sahayak Yojna. Immediately thereafter, Khattar was made Regional Sangathan Mahamantri for J&K, Punjab, Haryana, Chandigarh and Himachal Pradesh.
Khattar was BJP's Organizational Secretary in Haryana from 2000-2004.
For the 2014 Lok Sabha elections, Khattar was appointed chairman of the BJP's Haryana election committee.