Lavrov joked about Comey's firing as he entered an earlier meeting with Secretary of State Rex Tillerson.
Lavrov's visit was announced on Monday.
According to him, both meetings revolved around resolving the ongoing conflict in Syria and Tillerson's proposals for de-escalation zones in the country.
The Russian Foreign Ministry tweeted a photo of Trump and Lavrov shaking hands in the Oval Office, and another of Trump and Kislyak.
He also questioned why the firing was done in a seemingly "helter-skelter" fashion. Asked about Comey's firing at a briefing later, Lavrov said it was an internal United States matter and not for him to discuss. He raised his eyebrows.
The move provoked a storm of criticism among Democrats who said Trump was trying to blunt the Federal Bureau of Investigation probe, and some of the president's fellow Republicans also questioned the timing of the ouster.
After Tillerson visited Putin and Lavrov in Moscow on April 12, Trump said flatly, "Right now we're not getting along with Russian Federation at all".
The meeting with Lavrov was the highest-level public contact between Trump and the government of Russian President Vladimir Putin since Trump took office on January 20.
At Wednesday's meeting, Trump emphasized the need to work together to end the conflict in Syria, underscoring the need for Russian Federation to "rein in the Assad regime, Iran, and Iranian proxies". "Unfortunately the previous administration bent over backwards to undermine the solid foundation of those relations", Lavrov said, The Guardian reports.
Trump to meet top Russian diplomat at the White House
The White House closed off press access to the Oval Office meeting with Lavrov, and did not even allow photographers in. Trump made the comments during a surprise Oval Office meeting with former Secretary of State Henry Kissinger .
After the meeting, Lavrov spoke to the press, saying he and the president had spoken of issues concerning the Middle East and Ukraine, and had agreed to continue speaking and working together.
On the issue of anti-Russian sanctions, Lavrov said it was not discussed at the talks.
President Donald Trump could meet with Vladimir Putin's top diplomat at the White House on Wednesday, a US official and a person with knowledge of the plans said, describing what would be the highest level, face-to-face contact with Russian Federation of the American leader's young presidency. He and Lavrov said they discussed the civil war in Syria, where Russian Federation backs President Bashar al-Assad.
It is not known if the diplomats will discuss Russia's alleged meddling in elections in United States and Europe. That was the line Kremlin spokesperson Dmitri Peskov applied to the case of Comey Wednesday morning.
Russian President Vladimir Putin's spokesman says Moscow isn't concerned about the firing of the Federal Bureau of Investigation director.
"We believe the U.S. is really interested in that", Mr Lavrov said, acknowledging that details of the plan still needed to be worked out.
On the other hand, the White House clearly want nothing more than for Comey's dismissal to signal the end of the Russian Federation scandal. He said Wednesday he fired Comey because he "was not doing a good job".
Update, May 10, 2017, 11:42 a.m. ET: This piece was updated to include comments given by Trump and Lavrov.