Will pseudoephedrine hydrochloride affect a drug test?

Possibly: "false positive testing" occurs when a test finds evidence of illegal drug use when no drugs were taken. This can be a result of some over-the counter medications having chemical structures similar to illegal drugs. Pseudofed, found in many allergy and "cold" medications is one of these drugs.

It can: If it is a screening test, sudafed will often result in a positive amphetamine test. However, screening tests should be confirmed by more sophisticated testing, which will tell the difference between amphetamine and sudafed. If they are just doing a dipstick urine test (schools, employers etc often just do this), you may get into trouble for a false positive test.

Be prepared...: Based on the sophistication of the test, or lack of it, quite possibly.