The visit comes as previously icy relations between Cuba and the West are thawing, following the dramatic rapprochement between Havana and Washington in the last few months.
Mogherini will meet Cuban Foreign Minister Bruno Rodriguez during the two-day visit which "comes at a crucial time" for negotiations between the two sides, her office said yesterday ahead of her arrival, which was confirmed by a source close to the EU in Cuba.
The EU and Cuba held a third round of talks between chief negotiators at the beginning of March aimed at tackling sensitive human rights issues and finalizing an agreement "on political dialogue and cooperation."
No meeting with President Raul Castro has been announced.
Separately, Russian Foreign Minister Sergei Lavrov was also expected Tuesday in Havana.