"He arrived today" in his armoured train, Alexander Naryzhny, the head of the far eastern Khasan district which borders North Korea, told AFP.
It was Kim's first visit to Russia since 2002.
Kim is expected to meet with Medvedev for talks in the Siberian city of Ulan Ude near Lake Baikal. The Kremlin meanwhile declined to immediately confirm Kim's arrival.
North Korea's nuclear programme and closer economic ties are likely to be among the top topics on the agenda.
The visit comes as fears mount of a worsening hunger crisis in North Korea which threatens to affect hundreds of thousands of people.
The Russian foreign ministry said on Friday that Moscow was sending up to 50,000 tonnes of wheat to North Korea to help it cope with an "acute shortage of food supplies."
The first shipment arrived this week and the rest of the supplies would be sent next month, the foreign ministry said.
Officials in the Pacific region, including the governor and Kremlin's envoy, held a welcome ceremony for Kim in Khasan, said Naryzhny who also attended the event.
Kim, who is known to dislike air travel due to security concerns, arrived in Khasan district after crossing the Tumangan river at 12 pm local time (0100 GMT), Naryzhny said.
He said he was unaware of the North Korean leader's programme in Russia, adding he did not leave his train upon arrival.
South Korea's Yonhap news agency, citing informed sources, said Kim was expected to visit a dam in Ussuriysk, a town near Vladivostok, later in the day.
It said Kim would meet Medvedev in Ulan Ude on Tuesday, citing an informed source in Moscow.
Yonhap also said the North Korean leader may meet with both the Russian president and Prime Minister Vladimir Putin as he plans to remain in the country for about a week.
Kim and Medvedev were widely expected to hold a bilateral summit in or near the Russian Far Eastern port of Vladivostok earlier this summer.
A Kremlin official was quoted as saying at that time that Kim had cancelled his plans to come to Russia due to media leaks that he would be travelling.
Copyright AFP (Agence France-Presse), 2011