He attended a military meeting to hear reports from commanders, according to the Kremlin.
Mr Putin is also thought to have visited the Luhansk region. Russia annexed Kherson and Luhansk last year.
Such trips by the Russian leader are rare, although he made a surprise visit to the city of Mariupol in March.
Mykhailo Podolyak, an advisor to Ukrainian President Volodymyr Zelensky tweeted that Mr Putin was touring "the occupied and ruined territories" of Ukraine "to enjoy the crimes of his minions for the last time"."Putin's degradation is impressive," he said.
It is not known when the trip to Kherson took place but at one point in footage released of the trip, Mr Putin refers to the Easter holiday "coming up"- suggesting that it happened some days ago. Orthodox Easter was celebrated last Sunday.
But Kremlin spokesperson Dmitry Peskov has said that the trip happened on Monday and that Mr Putin's Easter comments had been misinterpreted, state media has reported.
The president is also said to have enquired about the situation in the Zaporizhzhia region, which Moscow has also claimed as part of Russia.
He is quoted as telling the military meeting in Kherson that while he did not want to distract them from their duties, "it is important for me to hear your opinion on how the situation is developing, to listen to you, to exchange information".
Russian troops retreated from the city of Kherson late last year, losing the only regional capital it had managed to capture since Moscow invaded Ukraine in February 2022.
In video released by the Kremlin, Mr Putin is seen stepping out of a helicopter in a field before it cuts to him getting out of a car and being greeted by a man in military uniform, thought to be military commander Col Gen Oleg Makarevich.
He is then filmed speaking in a control room, sat between Col Gen Makarevich and the head of Russia's airborne forces, Col Gen Mikhail Teplinsky.
Col Gen Teplinsky returned to the front line after allegedly being removed in January, American military experts and British intelligence have reported.
"Teplinsky is likely one of the few senior Russian generals widely respected by the rank-and-file," the UK Ministry of Defence wrote on social media on Sunday.
"His recent turbulent career suggests intense tensions between factions within the Russian General Staff about Russia's military approach in Ukraine."
Watch: Putin gives troops Russian Orthodox icon on visit to Kherson and Luhansk
Later in the video, Mr Putin presents what is reported to be a copy of an icon he says belonged to "one of the most successful defence ministers of the Russian Empire".
We see a road sign reading "see you later in the Kherson region" next to a hotel that has been verified by the BBC as being in the Kherson region. There are then aerial shots taken over a coastal village in the same area.
However, no shots in which the Russian president is filmed have been independently verified.
Afterwards, Mr Putin is seen getting out of a helicopter once again and is then shown in different clothes being taken into a bunker and speaking with Col Gen Alexander Lapin, chief of staff of Russia's ground forces.
The Kremlin says Mr Putin visited the Vostok headquarters, which belongs to Russia's National Guard, in occupied Luhansk.
It has also said that Russian Defence Minister Sergei Shoigu and Chief of the General Staff Valery Gerasimov did not accompany the president on the trip as it was a "big risk" for Russia's top commanders to be in one place so close to the front lines.