In 1980, the Janata Party split and the Bharatiya Janata Party (BJP) was formed. Rajagopal then served as its Kerala president until 1985. After 1985 he occupied a number of positions, including the All India Secretary, General Secretary, and the Vice-President of BJP. In 1989 he ran for a Lok Sabha from Manjeri but lost. Two years later, he contested in Thiruvananthapuram seat and lost again. His next run took place in the state of Madhya Pradesh. He was elected in 1992 and 1998 to the Rajya Sabha. In 1999 he attempted a second run from Thiruvananthapuram but failed again. However, he got a total of 1,58,221 votes (20.9%) and came second in one assembly segment out of seven. The total number of votes he secured was much higher than that for the previous BJP candidate in 1998 (94,303 votes, 12.3%) and 1996 (74,904, 10.4%) Lok Sabha elections.