He represented the Ellis Bridge constituency of Ahmedabad City as a Bharatiya Janata Party (BJP) legislator. He was a member of the RSS from his early age and was also a Municipal Councillor from the Paldi Area of Ahmedabad City. Pandya was a strong supporter of Keshubhai Patel and in 1998, after the BJP came to power in Gujarat with Keshubhai as Chief Minister, Pandya was made Home Minister of Gujarat. He was appointed as Minister of state for revenue after Modi took over as the Chief Minister; however, he resigned from the post in 2003. Fearing that he would be denied a ticket for the 2002 assembly elections, he withdrew from the electoral fray. Later he was appointed to BJP's national executive.
Haren Pandya wife Jagruti Pandya contested on Gujarat Parivartan Party ticket in 2012 on the premise that the Modi Government was involved in the conspiracy to murder her husband. She quoted "My husband's assassination was a political murder. For the last 10 years I have been fighting a legal battle to get him justice but in vain, however, I will continue to fight.
After the Godhra riots, it was reported that In a cabinet meeting, had opposed the bringing of the bodies of the victims of Godhra carnage to Ahmedabad because that would arouse passion. He was the only person able to arrange meetings between victim's family members and Muslim leaders for Peace talk but he was shouted down at the meeting by some ministers
In November 2007, Outlook reported that Pandya had revealed to the magazine in May 2002 that on the night of 27 February 2002 Narendra Modi had held a meeting in his residence in which he instructed the attending bureaucrats and police officers to allow "people to vent their frustration and not come in the way of the Hindu backlash." Pandya had disclosed this information on condition of confidentiality. On 19 August 2002, Pandya again spoke to the magazine, according to Outlook, and reiterated what he had said earlier with the additional comment that if his identity as the source of this information were to be revealed then he would be killed. The second conversation with Pandya was recorded by the magazine.
It has also been revealed that Pandya had testified before The Concerned Citizens Tribunal on 2002 Gujarat riots. Referring to Pandya's testimony, the tribunal's report says:
The tribunal received direct information through a testimony from a highly placed source of a meeting (on February 27, 2002) where the CM, two or three senior cabinet colleagues, the Ahmedabad police commissioner and an IG police were present. The meeting had a singular purpose: the senior-most police officials were told that they should expect a "Hindu reaction" after Godhra. They were also told they should not do anything to contain this reaction.
Hosbet Suresh, who was a member of the tribunal, has testified before the tribunal and that a recording of Pandya's testimony before the tribunal exists.
On 26 March 2003, at about 7.40 am Pandya was killed by two unidentified assailants who shot five bullets at him when he had just finished his morning walk in the Law Gardens in Ahmedabad. His body lay in his car for two hours. Pandya's family started worrying when he did not return home and sent his personal assistant Nilesh Bhatt to check on him. Bhatt found him lying dead in his car.
In 2007, a special POTA court had sentenced the main accused from Hyderabad, Asgar Ali, to life imprisonment, while handing out simple life imprisonment to seven others, 10-year jail term to two and five years imprisonment to one. They were all held guilty of murder and conspiracy to spread terror in Pandya murder case and attempted murder charges in the case of VHP leader Jagdish Tiwari. A lot of controversy followed his murder and top BJP Leaders such as Chief Minister Narendra Modi and the then Deputy Prime Minister of India Lal Krishna Advani were under intense criticism from within the Sangh Pariwar and General Public for sidelining Haren Pandya and not providing him proper security despite threats to his life and his request for security cover. Sanjiv Bhatt had even alerted Pandya about a threat to his life and even spoke out about Pandya to SIT probing Godhra riots.
On 29 August 2011 all the 12 people accused of murdering Pandya were acquitted of the murder charges by the Gujarat high court, but other charges including criminal conspiracy and attempt to murder were retained. The high court called the CBI's work a "botched up and blinkered" investigation.
In August 2011, DNA reported that Sohrabuddin Sheikh, a criminal who had earlier been killed by the Gujarat police in a false encounter, and his associate Tulsiram Prajapati may have been "used to kill Haren Pandya". Citing unnamed sources in the Gujarat State Police, the report said that Sohrabuddin was initially given the task but he back-pedalled and the murder was then executed by Tulsiram. In the encounter killings of Sohrabuddin and Tulsiram, the Gujarat state attorney K.T.S Tulsi has admitted before the court that these individuals were killed by the state police.
According to Sanjiv Bhatt, Pandya's murder was carried out by Tulsiram Prajapati as per what Bhatt was informed by Asgar, a criminal from Hyderabad. Asgar had informed Bhatt that he was contacted by Sohrabuddin Sheikh to carry out the murder, and had even visited Ahmedabad for this purpose, but at the last moment he had changed his mind and returned to Hyderabad without killing Pandya. Later Asgar came to know that the crime had been perpetrated by Tulsiram Prajapati, according to Bhatt.
D.G. Vanzara, the Gujarat police officer who had originally investigated the Pandya murder, and who has faced arrest and incarceration on charges of coordinating the Sohrabuddin and Tulsiram encounters, testified before the CBI in September 2013 about Sohrabuddin's role in Pandya's murder, and indicated a political conspiracy behind the killing.
In police terminology, the Pandya case has been called a "cut-out murder" in which it is not possible to establish the link between the victim and the conspirator or motivator of the crime. A police official offered this explanation:
A wants to murder Z and instructs B to execute the order. B tells C who does not know that A is the instigator. Instructions are passed in this manner from C to D and then to E and it goes down all the way. The final contract killer does not know where the order originated from. If investigations turns nasty, then all A has to do is to make any of the people in the chain a cut-out—take him out by beginning another chain.