ESPN and Major League Baseball appeared headed for an ugly separation after the network opted out of its rights deal in February.

Major League Baseball has completed new three-year media rights agreements with ESPN, NBCUniversal and Netflix NFLX -3.84%, the league is set to announce Wednesday.

As part of the rights agreements, which cover the 2026-2028 MLB seasons, the league’s longstanding relationship with ESPN will reach 39 consecutive seasons, NBC will return to regularly airing games o...