Lamu Senator Anwar Loitiptip lost his seat on Thursday, when the Court of Appeal determined that there irregularities in the August 8, 2017 poll.
Three Mombasa judges said the IEBC did not clear the irregularities before declaring the winner.
Judges Alnashir Visram, Martha Koome and Wanjiru Karanja also said election laws were defied.
The ruling followed a petition by Hassan Albeity who came second in the election with a vote difference of 58 votes.
Karanja, who read the judgment, said the High Court erred in validating Loitiptip's election despite the irregularities.
"We are satisfied that the appealant adduced enough evidence which should have called for a vote recount," she added.
The judge further said there was need to scrutinise votes at nine polling stations. She said were identified in line with the law and that the numbers at Kiangwe polling stations exceeded the number of registered voters.
Karanja told the IEBC and its officials to explain the disparity in the numbers and conduct a fresh election.
Earlier today, the Appeals court reinstated Bowen Kangogo as Marakwet East MP, saying he was rightfully elected.
A three-judge bench led by justice Erastus Githinji ruled that claims of massive irregularities and illegalities were not proved.