Flannery took over for longtime CEO Jeff Immelt in June 2017 with the company trying to re-establish its industrial roots, albeit a high-tech version of itself.
However, as Flannery has restructured the multinational conglomerate, its value has dipped below $100 billion and shares are down more than 35 percent this year.
GE warned Monday that it will miss its profit forecasts this year and it's taking a $23 billion charge.
The company said Monday that H. Lawrence Culp Jr. will take over as chairman and CEO immediately.
Shares of General Electric Co., based in Boston, surged 9 percent before the opening bell.