Clarke has been at the helm of the Southern Steel and Netball South since January 2013, and oversaw the transition to a zone-based model for the sport.
While she could not say exactly what ''business role'' she was moving into outside of sport, she will finish up on March 10, two weeks into the new ANZ Championship season.
''This is not a decision I made lightly,'' she said.
''I am a firm believer that one should never stop learning and the opportunity to embrace a new challenge and further my business skills was too hard to resist.''
Clarke was instrumental in making sure the transition into a zone-based sport went smoothly, but said it ''certainly'' had its challenges.
''I'm very proud of the progress which has been made across our zone,'' she said.
''Our netball community has really supported this new era and I'm confident the introduction of the Whole of Netball Plan developed by Netball New Zealand will bear fruit into the future and lead us in the right direction.''
The foundation of the plan sees New Zealand split into five zones: South, Mainland, Central, Waikato-Bay of Plenty and Northern.
Clarke's decision to leave after two years at the helm was made harder because of the staff who put ''a lot of energy'' into the new zonal system.
''I'm a loyal person at heart and my staff from the Steel and Netball South are of similar build and mould.
''That's the hard bit for me - saying bye to quality staff.''
Netball South chairman Paul Buckner said the board was ''very disappointed'' to lose a chief executive of Clarke's calibre, but supported her decision to move on.
As well crediting her for bedding down the new zone structure - an important link between the South zone and Netball New Zealand - he said Clarke met the challenges the job raised with ''fantastic'' energy, hard work and humour.
Buckner said the board would call on the expertise within the organisation to ensure minimal disruption until a new chief executive was appointed.
Clarke would not have any say in the appointment of her successor, and said it was unlikely a replacement would be found by the time she finished.
The recruitment process would ''hopefully'' start next week, she said.
