Yorkcourt wanted to create a base for a beer and wine making business on Newmarket Lane, which they said would create up to 130 jobs, but the proposal was rejected by a planning committee last week.
The company has faced heavy criticism from Wakefield Trinity fans for failing to build the new stadium the city expected when planning permission was granted for it in 2012.
And supporters welcomed last week's decision after they were outraged the warehouse application made no mention of when the 12,000 seater ground will be made a reality.
Members of the planning committee also accused Yorkcourt of "not caring" about Wakefield and "letting the city down".
In response, the applicants said the warehouse application was completely separate from the stadium issue.
Now, in a statement, Yorkcourt said: "While it’s disappointing that the application hasn’t been approved at this stage, we respect the decision taken and will continue to work closely with Wakefield Council and our development partner to find an acceptable solution.
"We remain committed to delivering this next stage of Wakefield Hub, which will safeguard jobs, while contributing to a dynamic and efficient local economy.”
Asked to clarify whether this meant Yorkcourt would appeal last week's decision, the company said they were "unable to comment further".
No appeal has yet been registered.
The firm also declined to answer whether or not they were still committed to building the stadium and wouldn't comment when asked why it hadn't yet been built.