It is the latest management upheaval at the firm after the heir of the entire Samsung Group was imprisoned for corruption in August.
His resignation comes on the same day the firm forecast record quarterly profits, citing higher memory chip prices.
"As we are confronted with unprecedented crisis inside out, I believe that time has now come for the company [to] start anew, with a new spirit and young leadership to better respond to challenges arising from the rapidly changing IT industry," he said in a statement.
Ryan Lim, founding partner of the Singapore technology consultancy firm QED said "Samsung is in a leadership crisis situation".
Mr Lim said "the current management structure seems to be a complicated web that does not clarify, but rather confuses".
"This needs to be resolved soon as it can be worrying not to know who is truly steering the Samsung behemoth into the future," he said.
In response to the criticism, a spokesperson for Samsung told the BBC that a successor would be appointed "soon" but could not give a timeframe.
Samsung Electronics is regarded as the jewel in the crown of the Samsung Group conglomerate, which is made up of 60 interlinked companies, and is one of South Korea's massive family-run businesses known as chaebols.
In August, the group's heir apparent Lee Jae-yong was convicted of bribery and corruption and sentenced to five years in jail.
Mr Lee is accused of giving donations worth 41bn won ($36m; £29m) to non-profit foundations operated by Choi Soon-sil, a friend of South Korea's former President Park Geun-hye, in return for political favours.
He was back in court on Thursday, appealing his jail term.