Defences were on top at the Weston Homes Community Stadium after Colchester striker Steven Gillespie had cancelled out Walker's early opener.
Colchester started well and Scunthorpe goalkeeper Sam Slocombe denied Scunthorpe pair Anthony Wordsworth and Lloyd James early on.
But Iron took an eighth-minute lead through Walker, whose shot deflected in off Colchester defender Tom Eastman after he had been picked out by Jordan Robertson in the penalty area.
Slocombe foiled Ian Henderson before Gillespie levelled for the U's in the 27th minute from the penalty spot, after being tripped by visiting defender Eddie Nolan in the area.
Slocombe almost allowed Gillespie's low shot to creep in just before the break, but Colchester goalkeeper Ben Williams denied Robertson early in the second half.
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