Ammonium and/or free ammonia (the unionized form of ammonium) are generally thought to inhibit the activities of microbes involved in anaerobic digestion of waste activated sludge. It was found in this work, however, that the presence of ammonium (NH4+-N) largely enhanced dark fermentative hydrogen production from alkaline pretreated-sludge. With the increase of initial NH4+-N level from 36 to 266 mg/L, the maximal hydrogen production from alkaline (pH 9.5) pretreated-sludge increased from 7.3 to 15.6 mL per gram volatile suspended solids (VSS) under the standard condition. Further increase of NH4+-N to 308 mg/L caused a slight decrease of hydrogen yield (15.0 mL/g VSS). Experimental results demonstrated that free ammonia instead of NH4+-N was the true contributor to the enhancement of hydrogen production. It was found that the presence of free ammonia facilitated the releases of both extracellular and intracellular constituents, which thereby provided more substrates for subsequent hydrogen production. The free ammonia at the tested levels (i.e., 0–444 mg/L) did not affect acetogenesis significantly. Although free ammonia inhibited all other bio-processes, its inhibition to the hydrogen consumption processes (i.e., homoacetogenesis, methanogenesis, and sulfate-reducing process) was much severer than that to the hydrolysis and acidogenesis processes. Further investigations with enzyme analyses showed that free ammonia posed slight impacts on protease, butyrate kinase, acetate kinase, CoA-transferase, and [FeFe] hydrogenase activities but largely suppressed the activities of coenzyme F420, carbon monoxide dehydrogenase, and adenylyl sulfate reductase, which were consistent with the chemical analyses performed above.