This study examined whether a three-month equine-assisted learning program improved measures of character skills in two independent cohorts of Year 1 youths, in a specialized secondary school for youths with difficulties coping with mainstream curriculum. In 2013, 75 students underwent intervention while 82 students did not. In 2014, 58 students underwent intervention and 59 students were waitlisted in semester 1; cross-over was performed in semester 2. The students were rated a week before, mid-way and a week post-intervention. Results from multi-level modeling indicated that the intervention led to progressive improvements in character skills over the school semester, in the majority of the constructs measured in both the 2013 and 2014 cohorts. The rate of change in measures of character skills over the semester correlated with the grade point average of the students at semester-end. Implications and limitations of the findings are discussed.