The 1963–64 Intertoto Cup was won by Slovnaft Bratislava who retained the trophy they had won the previous season, defeating Polonia Bytom in the final.

The tournament was expanded for this season, with 48 clubs entering compared to 32 in previous years, including the first clubs from Belgium to play in the Intertoto Cup - this meant an additional knock-out round was added between the Group Stage and the Quarter-Finals.

The groups were divided geographically as 'A', for Belgium, France, Italy and Switzerland; 'B' for Austria, the Netherlands, Sweden and West Germany; and 'C' for Czechoslovakia, East Germany, Poland and Yugoslavia.

The twelve group winners (shown in bold in the tables below) advanced to the knock-out rounds - where clubs from each of the three zones, 'A' 'B' and 'C', were kept apart.

1 Odra Opole progressed to the Semi-finals on a coin toss.