Each Member of Parliament has been ordered to return to exchequer Sh1 million that was paid as allowances.
On Thursday the National Assembly Clerk said that MPs will refund the money which the court ruled was illegally paid.
The Clerk dismissed claims that lawmakers received the pay for 5 months and not 2 years as reported.
A bench of three judges directed Senate and National Assembly clerks to recover the millions already paid out to each lawmaker within one year.
Court admonishes PSC
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The judges further faulted the Parliamentary Service Commission (PSC) for encroaching on the mandate of the Salaries and Remuneration Commission (SRC).
PSC had granted the lawmakers a house allowance of Sh250,000 and backdating it to 2018 in a move that saw each MP get Sh2.25 million.
Additionally, the judges said the Constitution and statutes do not give the PSC any specific function to set salaries and allowances of MPs and parliamentary staff.
Activist Okiya Omtatah and alongside other non-governmental organisations challenged the allowance in court, saying it was done by PSC without the approval of the SRC.