Madani (51), an accused in the 2008 serial blasts case, was accompanied by a team of police officials from Karnataka.
He had been permitted by the NIA court to visit his parents in Kerala.
The Supreme Court had permitted him to attend the wedding of his son on August 9 at Thalassery in Kannur district.
The court had criticised the Karnataka government for demanding Rs 14.8 lakh from the PDP leader to escort him to Kerala.
Hundreds of Madani's supporters had gatherred at Kochi International airport, where security was tight, to greet the PDP leader.
On his arrival, Madani said he was grateful to all those who had stood by him during his fight for justice.
While granting Madani the permission to visit Kerala to attend his son's wedding, the apex court had on July 31 asked him to bear the expenses incurred on his escort provided by the Karnataka police.
The PDP leader's visit had run into trouble after the Karnataka police sought Rs 14.79 lakh towards security expenses during his visit to Kerala.
During the first two visits, no amount was insisted on and in the third visit, Rs 50,000 was required to be paid.
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