EMC was set up by Frank Wimmer in 1995 and organises around 50 pharmaceutical events each year.
Wimmer will now become managing director of MCI Munich and said he was "very proud" to become part of MCI.
"The combination of expertise from EMC and MCI will increase synergies and significantly strengthen our position in Germany," he added. "Our combined market knowledge will be a great asset for all of our clients who will benefit from a global partner with international experience and standing."
MCI has around 45 offices around the world, including German sites in Berlin and Stuttgart.
The agency’s chief executive Se´bastien Tondeur said: "With MCI’s focus on pharma meetings, EMC is a great addition to our specialised offering. EMC’s team has clearly demonstrated its ability to deliver quality and a culture of winning."