The story of Rancho Santa Margarita began in 1882 when partners Richard O'Neill, Sr. and James Flood bought Rancho Santa Margarita y Las Flores in northern San Diego County and its adjoining Rancho Mission Viejo and Rancho Trabuco in southern Orange County. In 1943, upon the death of her husband, Richard, with the ranch lands held in trust, Marguerite O'Neill stepped forward to lead the family holdings. With great determination and pride, she kept the land intact and, as much as possible, in her family's control. To this day, Marguerite O'Neill's admonition to "take care of the land and the land will take care of you" continues to guide the family.

In 1986, a little over 100 years after attaining the ranch land, the O'Neill/Avery/Moiso families opened the beautiful 5,000 acre master planned community of Rancho Santa Margarita. The appeal of a safe, family oriented community located in the picturesque foothills of the Santa Ana Mountains soon brought hundreds of young families. It was in the spirit of a safe, vibrant, family oriented community that Melinda Heights Elementary School was born. Previously housed on the campuses of Cielo Vista and Trabuco Mesa Elementary Schools, the school's doors officially opened to 740 students in April, 1998. In the span of twelve years, the school's population has grown to over 1150 students instructed by 50 classroom teachers who are dedicated to the school's mission statement.