The pontiff also stressed on the urgent need to help "the most fragile people, innocent victims" of the full-scale invasion launched by Russia last year.
Mr Zelensky earlier met Italian Prime Minister Giorgia Meloni who assured him of Rome's support for united Ukraine.
More than 1,000 police are deployed and a no-fly zone over Rome is in place.
In a statement on Saturday, the Holy See said Pope Francis and President Zelensky "discussed the humanitarian and political situation in Ukraine caused by the ongoing war" during a meeting that lasted about 40 minutes.
The Argentine pontiff and President Zelensky "both agreed on the need to continue humanitarian efforts to support the population".
The statement added: "The Pope has assured his constant prayer and continuous invocation to the Lord for peace - since last February" - when Russian President Vladimir Putin ordered the full-scale invasion.
Pope Francis has often said that the Vatican stands ready to act as a mediator in the conflict between Russia and Ukraine.
Earlier this month, he stated that the Vatican was working on a peace plan to end the war, saying that the mission was "not yet public. When it is public, I will talk about it."
But the relationship between Ukraine and the Vatican has sometimes been uneasy.
A few months after the war in Ukraine began, the Pope said in an interview that Moscow's invasion was "perhaps somehow provoked".
And last August, Ukraine's ambassador to the Vatican took the unusual step of criticising the Pope after the pontiff referred to Darya Dugina, the daughter of a Russian ultra-nationalist figure, who was killed by a car bomb, as an "innocent" victim of war.
Earlier on Saturday, President Zelensky had talks with his counterpart Sergio President Mattarella and then met Ms Meloni for a working lunch.
Italy historically has strong ties with Moscow.
Silvio Berlusconi, leader of the conservative Forza Italia party, is an old friend of President Putin. They went on trips together and exchanged birthday gifts.
Matteo Salvini, the deputy prime minister, has frequently voiced pro-Russian sentiments and criticised military assistance to Ukraine. President Zelensky is not expected to meet either Mr Salvini or Mr Berlusconi during his trip.
At the news conference that followed the meeting between Mr Zelensky and Ms Meloni, the Ukrainian leader invited "all the Italian political leaders and representatives of civil society" to visit Ukraine.
He said they would be able "to see what a single person was capable of doing to us, what Putin was capable of, and you will understand why we are fighting this evil".
Ms Meloni stressed that the war would only end when Russia stopped its "brutal and unjust aggression" and withdrew from all Ukrainian territory.
She also pledged Italy's support for Ukraine for "as long as is necessary".
Meanwhile, the German government unveiled its biggest military aid package for Ukraine yet, worth €2.7bn (£2.4bn). Mykhailo Podolyak, an adviser to President Zelensky, said the aid indicated that Russia was "bound to lose and sit on the bench of historical shame".
Earlier this week, German media reported that President Zelensky was planning to visit Germany following his trip to Italy, although this has not yet been confirmed.
In other developments:
* President Zelensky's visit came after Russia carried out a new wave of air strikes on Kyiv and other Ukrainian cities overnight
* More than 20 people were injured in the western city of Khmelnytsky. Critical infrastructure, as well as homes and government buildings, was also hit
* Explosions were reported on Friday in the Russian-occupied city of Luhansk, about 90km (56 miles) behind the front line in eastern Ukraine. Russian-backed separatist forces in the region accused Kyiv of using Storm Shadow missiles, which the UK said it had supplied Ukraine with earlier this week
* There were also more reports of blasts in Luhansk on Saturday
* A helicopter crashed in Russia's Bryansk region, on the border with Ukraine, injuring one woman. Footage circulating on social media purports to show an S-24 war plane also crashing in the region on Saturday - although the videos have not been verified.