The study reveals the effect of work organization factors on operational excellence of small and medium enterprise in Kelantan. The work organization factors consist of transformational leadership style, human resource practices and organizational culture. A survey of a sample of Kelantan agriculture industry sector was conducted. Among the key findings, some of variable under work organization factors were a positive relationship towards on achievement of operational excellence. Conversely, there are also a variable under work organization factors were has not effect on the achievement of operational excellence of agriculture industry sector in Kelantan. Similarly, transformational leadership style and human resources practices were found to have an effect on the achievement of operational excellence for agriculture industry sector in Kelantan. In contrast, the analysis showed that involvement organizational culture has no significant relationship with operational excellence, therefore the hypothesis was not supported. The findings of this study contributed to a body of knowledge in terms of providing better understanding of the operational excellence in Malaysia SMEs industry. The practical adoption of managing the work organization among SMEs in Malaysia will contribute to the operational excellence in their business. Hence, added value to operational management paradigms to emerging in developing country context.