Control (Britain), George Smiley (Britain) and Karla (Soviet Union) in John le Carré novels.
Simon Illyan, head of ImpSec(Barrayaran Imperial Security) in the Vorkosigan Saga series.
X2, head of the secret service in Ibne Safi's Imran Series Novels. X2 is strict leader whose identity remains hidden from his team members and he makes contact with them on telephone or transmitter and at the same time he does all the field work along with his team mates being Ali Imran, a charming young man who looks like a moron and idiot by face. Due to his perfection in maintaining this dual personality, neither from his teammates, nor from his enemies could conclude that this Idiot Ali Imran could be the chief of secret service whose voice on a phone call could make his subordinate nervous.
Capt. Jacob "Ski" Strzeszewski – Fifth known S.H.I.E.L.D executive director. Former active S.H.I.E.L.D ground agent (Agent 10). Promoted through the ranks to become Head of Special Internal Operations for S.H.I.E.L.D.
William Walden and David Estes, the former/deceased Director of the CIA and Director of the Counter-terrorism Center, respectively, during seasons 1–2 of Homeland (TV series); throughout seasons 3, Saul Berenson was the acting-Director of the CIA.
Phillip "Phil" Coulson, after announcing his plan to go undercover for a while, General Fury hands Coulson the 'toolbox', a small cube containing coordinates and a few other things, and appoints Coulson acting Executive Director of S.H.I.E.L.D., with a mandate to rebuild the organization from the ground up.
Hiram Burrows is the Empire Spymaster in the game Dishonored, who later becomes the first Lord Regent, the main antagonist in the game.
Caius Cosades is the Imperial Grand-Spymaster of the Blades (who are an order of the Emperor's secret agents and protectors) in Morrowind, who acts as a guide, mentor and supervisor of the player character.