President Hage Geingob and Botswana's president Mokgweetsi Masisi had a closed-door meeting at State House in Windhoek on Sunday.
In a comment on Twitter, the Presidency said Masisi was in Namibia on a working visit to discuss matters of bilateral and regional concern.
On its part Botswana's presidency said the two heads of state discussed the official opening of the one-stop border crossing at the Buitepos and Mamuno border posts, which is to be known as the Trans-Kalahari-Mamuno checkpoint, later this year.
Geingob and Masisi also discussed matters pertaining to self-sufficiency in food production and the establishment of medical facilities in the Southern African Development Community region.
Namibia's deputy prime minister and minister of international relations and cooperation, Netumbo Nandi-Ndaitwah, also had a meeting with Botswana's minister of foreign affairs, Lemogang Kwape, during Masisi's visit to Windhoek.
Masisi and his team returned to Botswana after their meetings.