Shares in Nektan were trading down 18% at 29.70 pence on Thursday, following the news.
Nissim will remain with Nektan until August to ensure an orderly handover. The company didn't say where Nissim was going or what his new role would be.
Nektan said it has started the search for a permanent replacement, but in the meantime its founder and former CEO, Gary Shaw, will resume the CEO role on an interim basis.
"The company's trading continues to improve and the board expects to report positive quarter-on-quarter growth in the final quarter of the company's financial year to June 30, 2017. In addition, the company is in advanced discussions in respect of its funding, the details of which it expects to announce in due course," Nektan said in a statement.