IEBC Chairperson Wafula Chebukati has announced that the commission will contest Thursday's ruling.
The five judge bench gave 20 reasons why the entire process leading to the Constitution of Kenya (Amendment) Bill, 2020, was unconstitutional, null, and void.
Chief among them was that IEBC lacked quorum as specified in the constitution for purposes of carrying out referendum preparations, including verification of signatures.
But the High Court ruled that the IEBC was not properly constituted to conduct the exercise.
The bench also ruled that the Constitution of Kenya (Amendment) Bill, 2020, cannot be subjected to a referendum before the IEBC carries out nationwide voter registration.
This was raised since the IEBC has three commissioners instead of 7 as stipulated by the law. The Commission is made up of seven commissioners and a CEO appointed by them (who also acts as the commission secretary).
Earlier this year the electoral agency declared they had verified signatures in support of the Constitution of Kenya (Amendment) Bill, 2020 and they had surpassed the required one million mark.
The Bill was approved by more than 24 counties and introduced in the National Assembly and Senate where it received an overwhelming majority voted.
But the High Court bench which included Lady Justice Teresia Matheka, Justices George Odunga, Joel Ngugi (presiding), Jairus Ngaah and Chacha Mwita declared the Building Bridges Initiative (BBI) illegal, null and void.