An Israeli foreign ministry statement said Yair Lapid, who had been invited by his Bahraini counterpart, will inaugurate the Israeli embassy in Manama on Thursday and is "expected to sign a list of bilateral agreements".
"This will be the first official visit by an Israeli minister to (Bahrain)," the statement said.
The Israeli foreign minister touched down at Manama airport over an hour before a Gulf Air A320 took off in the opposite direction for the first commercial flight between the two countries.
Crew members waved the flags of Bahrain and Israel from cockpit windows of the passenger jet when it landed later at Ben Gurion airport near Tel Aviv.
The Bahrain flight and Israel's first bilateral ministerial visit to the Gulf country are part of a thaw in regional relations after the United Arab Emirates, Morocco and Sudan also agreed last year to establish ties with Israel under agreements known as the Abraham Accords.
"We've landed in Bahrain. I'm proud to represent Israel in an official and historic first in the kingdom. Thanks for the warm reception," Lapid said on Twitter.
Lapid met later with his Bahraini counterpart Abdullatif al-Zayani.
"We talked about the cooperation between our countries and about taking the official peace between us and turning it into an active, economic, security, political and civic friendship," he tweeted.
Following negotiations spearheaded by former US President Donald Trump, the United Arab Emirates, followed quickly by Bahrain and Morocco, last year became the first Arab states in decades to normalise relations with Israel.
The deals enraged the Palestinians, who felt a betrayal of their national cause. They saw it as an abandonment of a longstanding commitment in the Arab world not to normalise relations with Israel until there was progress in resolving the decades-long occupation of Palestinian land.