Samsung Electronics vice chairman Kwon Oh-Hyun will also resign as the chief executive of Samsung Display.
The decision comes after Jay Y Lee, who is heir to the Samsung empire, was jailed in August for bribery and perjury.
Oh-Hyun revealed his retirement In a letter sent to all employees.
He said: "It is something I had been thinking long and hard about for quite some time. It has not been an easy decision, but I feel I can no longer put it off.
"As we are confronted with unprecedented crisis inside out, I believe that time has now come for the company start anew, with a new spirit and young leadership to better respond to challenges arising from the rapidly changing IT industry."
Oh-Hyun has worked at Samsung for 32 years and said "there are no words to describe how proud I am that we built together one of the most valuable companies in the world".
He added: "But now the company needs a new leader more than ever and it is time for me to move to the next chapter of my life."