She has the led the conservation charity for 15 years and will leave in October. Under her leadership, The Wildlife Trusts successfully campaigned for the Marine and Coastal Access Act 2009.
Peta Foxall, chair of The Wildlife Trusts, said Hilborne was leaving the charity in "good heart", having strengthened its governance and central team and increased its external influence over the past 15 years.
"The movement has grown its impact in this time, delivering outstanding programmes ranging from large-scale habitat restoration to ecotherapy," he said.
"The policy and legislative changes that The Wildlife Trusts has contributed to during Stephanie’s tenure will lead to real gains for wildlife."
Hilborne said in a statement: "Never has the world been more conscious of the scale of the ecological crisis and never has our movement had so much relevance, as a new generation takes up the helm. I wish all my friends in the movement well as they go from strength to strength."