Students outside the auditorium also chanted anti-Comey slogans, including "get out Comey, you ain't my homey".
Comey will announce the topic of the lectures after consulting with student leaders and other campus stakeholders on topics relevant to the Howard community.
"I'm honored to be here and I'm looking forward to adult conversations about what is right and what is true", Comey said at the conclusion of his remarks.
In June testimony before a congressional panel, Comey accused the president of firing him in May to try to undermine the FBI's investigation of possible collusion by Trump's campaign with Russia's alleged efforts to influence the 2016 election.
However, despite opposition to Comey's role at the school, notable Howard alumni including writer Ta-Nehisi Coates, and congressman Elijah Cummings both come out strongly in favor of the appointment.
"I'm only going to speak for 12 minutes, " he said.
Comey said he appreciated the protesters "enthusiasm" but wishes they could understand "what a conversation is". But the group continued.
Comey was set to speak at Howard's 2017-18 convocation as the school's endowed chair of public policy, but he didn't receive a warm welcome from some students at the historically black college.
In a statement, Howard University President Wayne A.I. Frederick called Comey an ethical man who wants to challenge students to be more open to people who have different views.
"What does Comey have to tell me about being a black woman?" she asked.