Saturday's visit by Afwerki, his first in 20 years, comes a week after Ethiopia's Prime Minister Abiy Ahmed made a landmark visit to Eritrea's capital, Asmara.
An agreement signed in Asmara by the two Horn of Africa nations on Monday formally ended a conflict that has been ongoing for more than two decades.
The newly-appointed reformist Abiy first instigated the peace overtures and restoration of relations in April.
Many observers have been caught by surprise.It all started when Prime Minister Abiy reached out to the Eritrean president back in April and agreed to abide by the UN ruling on the disputed territories that have been the cause of this 20-year conflict.
This visit by President Afwerki really cements this thawing of relations. We expect a lot of Ethiopians to receive the president. It's very good news all around.
As part of the thawing of relations, Ethiopian Airlines is due to resume commercial flights to Asmara on Wednesday.
It is still too early to tell how the new relationship will affect lasting peace in the region, but she said that it is certainly hugely significant for the stability of the region.
Both Eritrea and Ethiopia are expected to benefit from renewed trade ties between the two nations. Ethiopia, a landlocked country, will start using the ports of Eritrea, which will increase turnover.
