Does it matter what time of the day you take a pregnancy test five weeks after the encounter?

Yes: The more concentrated the urine specimen, the more likely to detect even low levels if the hormone HCG which signals a positive pregnancy test. Test with the first morning urine. It is sometimes more accurate to collect urine in a disposable cup and hold the test in the cup for the alotted time versus holding it in the urine stream. It ensures the entire strip gets appropriately saturated.