pH-weighted amide proton transfer (APT) MRI is promising to serve as a new surrogate metabolic imaging biomarker for refined ischemic tissue demarcation. APT MRI with pulse-RF irradiation (pulse-APT) is an alternative to the routine continuous wave (CW-) APT MRI that overcomes the RF duty cycle limit. Our study aimed to generalize the recently developed pH-specific magnetization transfer and relaxation-normalized APT (MRAPT) analysis to pulse-APT MRI in acute stroke imaging. Multiparametric MRI, including CW- and pulse-APT MRI scans, were performed following middle cerebral artery occlusion in rats. We calculated pH-sensitive MTRasym and pH-specific MRAPT contrast between the ipsilateral diffusion lesion and contralateral normal area. An inversion pulse of 10 to 15 ms maximizes the pH-sensitive MRI contrast for pulse-APT MRI. The contrast-to-noise ratio of pH-specific MRAPT effect between the contralateral normal area and ischemic lesion from both methods are comparable (3.25 ± 0.65 vs. 3.59 ± 0.40, P > .05). pH determined from both methods were in good agreement, with their difference within 0.1. Pulse-APT MRI provides highly pH-specific mapping for acute stroke imaging.