His wife, Harjeet Kaur, had sought his release on parole for three weeks for him to take care of his ailing mother Naseeb Kaur who is 85.
The court was of the opinion that Ram Rahim could himself file the plea.
The parole was sought on the grounds that the convict had earned "good conduct remission reports".
The court reportedly rapped the petitioner saying Ram Rahim's mother should be treated at the large hospital run by his sect. It also said that his family was already living with his mother to take care of her.
Earlier, jail authorities in Rohtak, where Ram Rahim is serving his sentence, had refused to grant him parole to meet his ailing mother.
The decision not to grant parole was taken by Jail Superintendent Sunil Sangwan on August 9 after Justice Kuldip Singh of the Punjab and Haryana High Court directed the state to take a decision on the representation by Ram Rahim's wife.
She moved the parole plea saying that Ram Rahim's mother was suffering from heart disease and she was not taking treatment in the absence of her son.
Ram Rahim (51) is currently lodged at the high-security Sunaria jail in Rohtak, 250 kms from Chandigarh.
Ram Rahim had withdrawn his parole plea in June at the last minute after the state BJP government was cornered by opposition parties for favouring the sect chief who had sought a parole of 42 days for tending to the sprawling fields in his sect's headquarters in Sirsa town.
Before that the high court had in May rejected Ram Rahim's parole plea for attending the wedding ceremony of his foster daughters.
Ram Rahim was sentenced to 20 years in jail in August 2017 for raping two women.
A special CBI court in Panchkula this January also sentenced him and three others to life imprisonment for the murder of a journalist over 16 years ago.
In jail Ram Rahim spends most of his time growing vegetables and fruits and daily earns Rs 20 for eight hours of farming which comes under the unskilled work category.
As per the jail superintendent, Ram Rahim's conduct in jail is like a "disciplined inmate".
His conviction on August 25, 2017 had led to violence in Panchkula and Sirsa, leaving 41 people dead and over 260 injured.
Ram Rahim was patronised by political leaders and parties in Punjab and Haryana for nearly two decades due to his ability to influence the votes of his followers.
( With inputs from IANS )