Currently, the deadline for this has not been set by the government although those who have filed ITR for FY16-17 are required to do the same by March 31, 2019.
With the Supreme Court (SC) upholding the government requirement that PAN must be mandatorily linked with Aadhaar, Section 139AA of the Income Tax Act comes into play. As per this section, if your PAN is not linked with Aadhaar by a date to be notified by the government then it would be deemed to become invalid. Currently, the deadline for this has not been set by the government although those who have filed ITR for FY16-17 without linking PAN with Aadhaar are required to do the same by March 31, 2019.
Shalini Jain, Tax Partner, People Advisory Services, EY India says, "The deadline of March 31, 2019 to link PAN with Aadhaar is relevant for those taxpayers who have filed their income tax return (ITR) for FY2016-17 (AY2017-18). Without linking the same - their returns will not be processed unless the linking is done by 31 March, 2019. However, those taxpayers who have filed the returns for FY 2016-17 or FY 2017-18 by linking PAN with Aadhaar need not worry about the March 31 deadline. Technically, for individuals, who have not filed their ITR for FY 2016-17 and FY 2017-18 and are yet to link their PAN with Aadhaar are not impacted by March 31, 2019 deadline as the government is yet to notify the last date for PAN Aadhaar linkage. Since as per Section 139AA, it is mandatory for every individual having PAN to link with Aadhaar, it is advisable to do the same as soon as possible."
Sooner or later the government will set the deadline for all PAN holders to link the same to their Aadhaar as an enabling provision has already been incorporated in section 139AA of the Income Tax Act. Therefore, it would be advisable to link the two. If you have done so and want to make sure that the two identity numbers are linked in the income tax department's database, here is how to do it.