After receiving his passport from a local court in Ajmer, Chisti boarded Shatabdi Express along with his brother Jamil Chisti and others and reached New Delhi rail station at around 11 PM.
Chisti said he would also go to Lahore to meet Sarabjit Singh, an Indian national who is languishing in a Lahore jail in Pakistan for the last 22 years.
82-year-old Chisti is facing life sentence in a murder case. He was on May 10 permitted by the Supreme Court to visit Pakistan for a temporary stay.
"I am happy that I am going to my home land to meet my family and friends. I would like to offer thanks giving prayer as soon as I reach airport, and thereafter I will go to my home," Chisti told reporters after the train reached Jaipur railway station.
"Being a Muslim its my duty to thank God. I will meet my family, children wife and my friends and those who come to see me. When I am in Pakistan, I would like to visit the whole of the country. I would like to go to Lahore and meet Sarabjit Singh," he said.
A PUCL activist who is accompanying him said that Chisti will go to the Pakistan High Commission in Delhi tomorrow and after completing remaining formalities, he will take a flight for Pakistan.
As per the apex court's direction, Chisti will have to deposit his passport at the Indian High Commission in Pakistan and return to India by November 1.
Chisti came to Ajmer in 1992 to visit his ailing mother. However, he allegedly got himself involved in a brawl in which one of his relatives was killed.
The apex court granted him bail on April 9 and since then he was living with his brother's family in Dargarh area in Ajmer.