JEE (Joint Entrance Examination) is a two tier examination (Main & Advanced) regulated by CBSE Board.

As you asking here I am telling application fee payment can be made:

(a) by credit/debit card, or
(b) by demand draft (DD) issued by a scheduled commercial bank in favour of Secretary, CBSE, payable at Delhi.

Executive Director
JEE (Main) Secretariat
Central Board of Secondary Education,
PS-1-2, Institutional Area,
I.P.Extn. Patparganj, Delhi-110 092.

Application Fee:
Papers Pen & Paper Based Test Online mode
Appearing General/OBCs (Boys) SC/ST/PWD/All Girls General/OBCs SC/ST/PWD/Girls

For examination centres opted in India
Paper 1 or 2 1000 500 500 250
Paper 1 and 2 both 1800 900 1300 650

For examination centres opted in foreign country
Paper 1 or 2 2500 1250 2500 1250
Paper 1 and 2 both 3800 1900 3800 1900

Key dates
Notification release – 18th November 2016
Application form begins – 1st December 2016
Application form end – 16th January 2017
Last date of Payment – 18th January 2017
Correction in application form – 25th January to 3rd February 2017.
Admit card release – 14th April 2017
Offline exam date – 2nd April 2017
Online exam date – 8th and 9th April 2017