Foreign minister Falconi gave Mr Sullivan 48 hours to leave the country
Ecuador has expelled a second American diplomat in just over a week, accusing both officials of interfering in its internal affairs.
Foreign Minister Fander Falconi said Mark Sullivan, the first secretary at the US embassy in Quito, had 48 hours to leave the country.
Both US officials were accused of meddling with police appointments in a US-funded anti-narcotics programme.
Washington has rejected the charges and called the expulsions unjustified.
Last week, Ecuadorean President Rafael Correa ordered US customs attache Armando Astorga to leave on similar charges.
It accused Mr Astorga of being "insolent and foolish" and said he had treated Ecuador like a colony by trying to dictate the Ecuadoran police's choice of a commander for an anti-smuggling unit in return for $340,000 in US aid.
The Ecuadorean government accused Mr Sullivan of trying to do the same thing.
"Following the Astorga affair, Sullivan also placed conditions on logistics cooperation with the police," Mr Falconi said.
An unnamed US state department official told AFP news agency that the US is required by law to vet candidates for US-funded training programmes.
"We regret this decision by the government of Ecuador. We also reject any suggestion of wrongdoing by embassy staff," said state department spokesman Gordon Duguid.
"Despite the government of Ecuador's unjustified action, we remain committed to working collaboratively with Ecuador to confront narcotics trafficking," he added.
BBC South America correspondent Candace Piette says the president is in full campaign mode ahead of elections in April.
She says Mr Correa is extremely popular at the moment, and the message of strong Ecuadorean sovereignty and intolerance of American interference goes down well with the public.
President Correa has clashed with Washington over several issues - most notably refusing to renew the lease on airbases used by US forces to mount anti-narcotics missions.
But compared with other left-wing governments in Latin America, the rows between Quito and Washington have been low-key.