Much of the current academic literature on the practice of homeschooling has revolved around the individual academic, social, and psychosocial outcomes of homeschooled youth. As such, the relational and systemic implications of homeschooling have been neglected in the current body of research, thus leaving the practice’s long-term outcomes on family and relational functionality up to heuristic assumption by homeschooling families and the general public. The current study sought to address this gap in the literature by introducing a family systems perspective to the assessment of homeschooling families and homeschooler’s relational functionality. Comparisons between homeschooled (n = 145) and non-homeschooled (n = 147) adults found that, after controlling for demographic differences, homeschooled adults reported that their families had higher levels of unbalanced Enmeshment and Rigidity, along with lower levels of unbalanced Disengagement, than non-homeschooled participants within the Circumplex Model of Marital and Family Functioning. Homeschoolers also displayed greater levels of Differentiation-of-Self in the domains of Emotional Reactivity and I-Position taking than non-homeschoolers. These results, however, were found to be closely connected to homeschooled participants’ reports of how many years they were homeschooled, the degree of structure in their homeschooling environment, as well as the strength of several different common rationales they believe motivated their family to choose to homeschool, with certain factors emerging as significant predictors of whether homeschoolers reported a more functional family environment and higher Differentiation-of-Self. The clinical and research implications, limitations, and future directions for studies of this kind, are discussed.