The firm, which has 550 UK stores and 4,000 employees, said Nick Davis would leave immediately to “pursue other business interests”.
It blamed “tough” trading conditions since May for the profit warning.
Mr Davis will be replaced by the firm’s executive chairman Anthony Smith.
“As has been widely publicised, the UK High Street is currently facing a challenging environment in which to operate,” he said.
As a result, Mr Smith said he would focus attentions on online and larger out-of-town stores.
- Why the High Street crisis could worsen
The company also revealed that its freehold property portfolio was worth £3.1m less than expected, and will write down the value of its 17 freehold properties to £5.3m. It blamed a “tough” property market for the decision.
The number of empty shops in Britain hit its highest rate in four years in July as shopper footfall fell by 1.9%, the worst decline in seven years.
But Shoe Zone said there was an upside to the difficult trading conditions on the High Street.
“The pressure on the retail property market has enabled Shoe Zone to achieve an average 23.5% fall in rents on renewal and average outstanding lease length of only two years,” Mr Smith said.
The firm’s shares fell as low as 116.6p in early trading on Friday, well below the 160p they were valued at when the company listed in 2014.