The president unfurled the Kenyan flag aboard a tanker at the Indian Ocean port of Mombasa that will be carrying the oil to Asia.
"There are special moments that mark a turning point in the destiny of our nation," Kenyatta said at the ceremony.
"The first export of crude oil by our nation, therefore, marks a special moment in our history as a people and as a country."
The maiden shipment was purchased for USD$12 million (10.8 million euros) by Chinese trading company ChemChina for export to Malaysia.
Kenyatta said the first attempts at finding oil in Kenya date back to 1937 but it was not until 2012 that a commercially-viable deposit was located.
This field was discovered in the South Lokichar Basin in Turkana, in Kenya's far north, by British firm Tullow and its joint venture partners.
The company estimates the field holds 560 million barrels of oil.
