Miguna was deported, for the second time, on March 29 after spending more than 72 hours in a tiny room at the JKIA.
Judge Enoch Chacha Mwita says his deportation was unlawful and in violation of the Constitution.
The judge adds that the lawyer did not lose his citizenship upon acquiring a Canadian passport.
A Kenyan court has awarded opposition firebrand Dr Miguna Miguna Ksh7 million ($70,000) as compensation for the violation of his rights during his deportation to Canada.
In the ruling on Friday, High Court Judge Enoch Chacha Mwita said Mr Miguna's deportation was unlawful and in violation of the Constitution.
Concerning Mr Miguna's passport, Justice Mwita said its cancellation and the declaration that he was a prohibited immigrant was unconstitutional.
The judge declared this decision null and noted that if the lawyer had to be sent away, the process should have been carried out in line with the Fair Administrative Act.
"I find and hold that he did not lose his citizenship upon acquiring a Canadian passport," said Justice Mwita.
"He was entitled to due process and I hereby award him Ksh7 million for violation of his rights."
The judge also lashed out at Interior Cabinet Secretary Fred Matiang'i and Inspector General of Police Joseph Boinnet for violating the law as well as denying Mr Miguna a fair hearing.
In May, the fiery lawyer said he wanted to be granted unconditional re-entry into the country.
In a fresh application filed by his lawyers, the opposition politician faulted the government for failing to facilitate his return and entry into Kenya.
Mr Miguna was deported, for the second time, on March 29 after spending more than 72 hours in a tiny room at the Jomo Kenyatta International Airport (JKIA) after authorities denied him entry into the country.
It was not long after Orange Democratic Movement leader Raila Odinga's mock oath that Mr Miguna was arrested, detained and eventually deported.
The government claimed he was a Canadian national, arguing he never re-applied for his Kenyan citizenship after the promulgation of the 2010 Constitution.
The Kenyan-Canadian deportee listed Kenya Airports Authority, Mr Matiang'i, Mr Boinnet, the GSU commandant, JKIA OCS or any other, the Flying Squad boss, Kenya Police and the Attorney General as the officials and entities he wants compelled to aid his unfettered return.
