In October last year, the government lifted a decade-old ban on GM crops in response to dwindling food security following the worst drought to ravage the Horn of Africa region in 40 years.
Kenyan lawyer Paul Mwangi swiftly launched a court challenge, arguing the decision was unconstitutional as there were concerns over the safety of the crops.
But environment court judge Oscar Angote ruled on Thursday that there was no evidence to show any harm to nature or human health.
"As a country, we need to trust the institutions that we have in place and call them to order when they breach the law," Angote said, making reference to government bodies that regulate GM foods.
"We should be confident that our health is in good hands."
There was no immediate response about the ruling from Mwangi, a lawyer who is close to the opposition.
Kenya, like many other African nations, banned GM crops over health and safety concerns and to protect smallholder farms, which account for the vast majority of rural agricultural producers in the country.
However, the East African powerhouse faced criticism over the ban including from the United States which is a major producer of GM crops.
Activists and agriculture lobby groups have protested over the lifting of the ban, saying it opened the market to US farmers using sophisticated technologies and highly subsidised farming that threatened the livelihoods of small-scale farmers.
Agriculture is the biggest single contributor to Kenya's economy, generating more than 21 percent of gross domestic product (GDP) last year, according to government figures.
The agricultural sector employs about 12 percent of Kenya's 19 million workers, behind the education sector and manufacturing.