The Foundation offers a unique program that presents its participants with a new direction in life. Teams trek 100km through the spectacular Flinders Ranges with the aim to develop personal attitudes of self esteem, leadership, motivation, team work and responsibility. They learn basic bush survival skills, are taught to abseil, discover Indigenous culture and learn of the rich history of the Flinders Ranges. Unlike other aspects of their lives, there is not an opportunity for the participants to 'opt out'.

Each team, of between 8 and 10, is led by an experienced team leader who is often a serving or retired army or police officer skilled in navigation and bushcraft. The young participants live out and sleep on the ground, prepare their own food, navigate through the Flinders Ranges and learn the values of team work and respect.

An independent evaluation in 2001 reported that the program at that time lead the world in its outcomes, and found that the young people at high risk underwent a significant positive change as a result. Operation Flinders fields teams from both metropolitan and regional communities throughout South Australia. In the year 2007, a record number of 345 young people participated in an Operation Flinders Foundation Exercise.

A key objective of the Foundation is to effect a positive life change for young people at risk by improving self esteem and confidence, increasing the rate of return to education, encouraging young participants to seek employment, or positive opportunities, in their local communities. The Operation Flinders Foundation program gives young people at risk a second chance at life.