This is an alphabetical list of NAIA Division II conferences. It will be maintained concurrently with the equivalent category.

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• American Mideast Conference
• Appalachian Athletic Conference
• California Pacific Conference
• Cascade Collegiate Conference
• Chicagoland Collegiate Athletic Conference
• Dakota Athletic Conference
• Florida Sun Conference
• Great Plains Athletic Conference
• Heart of America Athletic Conference
• Kansas Collegiate Athletic Conference
• Kentucky Intercollegiate Athletic Conference
• Mid-Central College Conference
• Midlands Collegiate Athletic Conference
• Midwest Classic Conference
• NAIA Division II Independents
• Sunrise Conference
• Wolverine-Hoosier Athletic Conference