The plaque was part of River of Life, a fountain with a base showing children's handprints. Police said the plaque disappeared sometime between April 20 and May 5, The Daily Telegraph reported.
"This plaque forms part of a memorial and is of great significance to the town," said Constable Graham Davies of the Cheshire Police. "It is upsetting for people to see that the plaque has been taken."
Warrington, an old industrial town between Liverpool and Manchester, was hit by two bombs March 23, 1993. Scores of children in a McDonald's Restaurant were injured, and Johnathan Ball, 3, was killed.
Tim Parry, 12, died five days later.
Tim's parents, Colin and Wendy Parry, founded a Peace Center in Warrington and became actively involved in the Northern Ireland peace process.
A man was charged with trying to steal the plaque in April.
Thefts of potentially valuable metal objects have become a major problem in England. Police in London made several arrests this week in a series of raids on scrap yards, the Evening Standard reported.
One yard yielded an especially rich haul. In addition to scores of memorial plaques from graveyards and crematoriums, investigators found a 1-ton ornamental dragon taken from a suburban London garden, a large cross and a full-size statue of Jesus Christ.