The 1946 New Mexico Lobos football team represented the University of New Mexico in the Border Conference during the 1946 college football season. In their fifth and final season under head coach Willis Barnes, the Lobos compiled a 5–5–2 record (4–2–1 against conference opponents), finished third in the Border Conference, tied with Montana State in the 1947 Harbor Bowl, and were outscored by opponents by a total of 224 to 127.