Caniff was one of the founders of the National Cartoonists Society and served two terms as its president, 1948 and 1949. He also received the Society’s first Cartoonist of the Year Award in 1947 for work published during 1946, which included both Steve Canyon and Terry and the Pirates as well. Caniff would be named Cartoonist of the Year again, receiving the accompanying trophy, the Reuben, in 1972 for 1971, again for Steve Canyon. He was awarded an Inkpot Award in 1974.

He was inducted into the comic book industry’s Will Eisner Comic Book Hall of Fame in 1988. He received the National Cartoonists Society Elzie Segar Award in 1971, the Award for Story Comic Strip in 1979 for Steve Canyon, the Gold Key Award (the Society’s Hall of Fame) in 1981, and the NCS has since named the Milton Caniff Lifetime Achievement Award in his honor.

In 1977, the Milton Caniff Collection of papers and original art became the foundation for what is known presently as the Billy Ireland Cartoon Library & Museum. Covering 696 cubic feet (19.7 m3), the collection fills 526 boxes, plus 12,153 art originals and 59 oversized items. In addition to the original artwork, the collection includes Caniff’s personal and business papers, correspondence, research files, photographs, memorabilia, merchandise, realia, awards, audio/visual material and scrapbooks.

In 1987, he was made the first honorary member of the Eighth Air Force Historical Society in recognition for the “Male Call” strip that he did for Stars and Stripes during World War II.