The one-day trip comes a month after Alexis Tsipras and his Skopje counterpart Zoran Zaev finalised the deal that added "North" to Macedonia's name to distinguish it from a bordering province in Greece.
It is the first official visit by a Greek prime minister since the former Yugoslav republic declared independence in 1991, kicking off the name row that roiled diplomatic ties for nearly three decades as the neighbours tussled for ownership of the name Macedonia and its cultural heritage.
In the end, Skopje agreed to the change in exchange for assurance that Athens would stop thwarting its efforts to join NATO and the European Union.
"The first prime minister of Greece to visit North Macedonia. Truly historic day," Zaev wrote on Twitter beneath a photo of the two leaders embracing outside the government building, where they took a selfie before entering inside.
VIDEO: North Macedonia Prime Minister Zoran Zaev says his country is welcoming "big (Greek) companies with billions in annual revenues" after its name-change deal with Greece, on the eve of a landmark visit from his Greek counterpart Alexis Tsipras in Skopje pic.twitter.com/iKCQsw70kdAFP news agency (@AFP) April 2, 2019
With the name issue behind them, the neighbours are also touting the promise of boosting economic ties.
Tsipras is joined by 10 ministers and more than two dozen Greek business leaders with him who will attend a business forum in the afternoon.
Ahead of the visit, Zaev told AFP there would be new Greek investments worth more than 500 million euros in North Macedonia, which is much smaller and poorer than its EU member neighbour.
"The Republic of North Macedonia will have huge economic benefits from the deal that I believe will be seen in every area of the economy," the prime minister added.
Since the initial name accord was inked in June 2018, congratulations have poured in from around the globe for the two young premiers, who took on risky political battles at home to push the deal through, enraging nationalists in both countries.
Even before the deal was finalised, the pair were nominated for the Nobel Peace Prize by 2015 winner Wided Bouchamaoui of Tunisia.
"This visit is historic," Tsipras told the state-run MIA news agency on Monday, hailing a new future for the "partners and allies".
But he conceded that a "significant portion of the Greek people" are still "seriously concerned" about the name deal.
"It is our responsibility -- mine and Zoran's -- to show that our nations can only benefit from the path that is now open," he said, condemning "rising forces of nationalism".
Disgruntlement is also palpable in Skopje among some who feel the name-change is an embarrassing concession to Greece and that the end-goal -- entry into the EU -- may never materialise.
North Macedonia is in the process of joining NATO and hoping the EU will open accession talks in June.
Yet the timeline is unclear, with appetite for enlargement shrinking considerably among several members of the bloc, particularly France.
Meanwhile, in his own protest, the Balkan state's President Gjorge Ivanov has been refusing to sign bills from parliament ever since North Macedonia became the official name.
The two-term president will be replaced in elections later this month.