Introduction Bacteriological examination of sputum is the cornerstone in the diagnosis of pulmonary tuberculosis in the developing world. The risk of spread of infection and emergence of drug resistant strain has created the need of rapid, sensitive and specific diagnostic test. Objectives This prospective study was performed in Tuberculosis research laboratory, Department of Microbiology, BPKIHS, Dharan with an objective to evaluate different staining techniques (Ziehl-Neelsen (ZN), Kinyoun, Modified cold (MC), Fluorochrome) for detection of acid fast bacilli (AFB) for diagnosis of pulmonary tuberculosis. Methods The study was cross-sectional study. All the samples were processed by modified Petroff’s method. From each sample four smears were prepared and were stained with four different staining techniques: ZN, Kinyoun, MC, and Fluorochrome respectively. Culture was employed as gold standard for tuberculosis diagnosis. Results A total of 1365 specimens from 500 patients were analyzed. One hundred nine patients (21.8%) were diagnosed as having TB by culture. The positive yield found with the staining techniques were 14.2 percent by ZN, 13.8 percent by Kinyoun, 14.4 percent by MC and 17.6 percent by Fluorochrome staining methods. With reference to culture, sensitivity of ZN, Kinyoun, MC and Fluorochrome were found to be 57.8 percent, 56 percent, 59.6 percent, and 71.6 percent respectively. The specificity in ZN, Kinyoun and Fluorochrome methods was 98 percent and that in MC as 98.2 percent. The positive predictive value of ZN, Kinyoun, MC, Fluorochrome was found to be 88.7 percent, 88.4 percent, 90.3 percent and 90.7 percent and the negative predictive value of ZN, Kinyoun, MC, Fluorochrome was found to be 89.3 percent, 88.9 percent, 89.7 percent and 92.5 percent respectively. Conclusion The fluorescent staining method was found most reliable out of the other staining techniques. The MC method also could be viable alternative to ZN and Kinyoun for primary diagnosis of tuberculosis.