Jim McFarlane, founder of Livingston-based Endura, said some of the work done on the company's West Lothian site would most likely relocate to the Czech Republic if there is a Yes vote next month.
He has also put plans to expand the warehouse facility at the site on hold until after the referendum.
Endura, which was set up in the 1990s, sponsors and provides racing kit for two of the top road racing teams, Movistar and Net App Endura.
The firm, which employs almost 200 people in total, also kits out cycling clubs across the UK and makes clothing for those who commute to work by bike or simply cycle for leisure.
Mr McFarlane said: "We've been building jobs up in this area for nearly 20 years and it's galling to have to consider exporting jobs rather than our products."
With Endura selling much of the cycling equipment it produces overseas, his key concern is Scotland's continuing membership of the European Union.
Mr McFarlane said: "We have multiple bank accounts and deal in multiple currencies, so something like currency is less of an issue for us.
"What we are primarily concerned about is having continued, unbroken membership of the European Union (EU).
"From this site here we dispatch a couple of hundred orders a day to bike shops across Europe.
"We're concerned about what would happen if there was any break in smooth trading with the EU."
He added: "I'm not saying we wouldn't get in but there is substantial uncertainty about when we would get in and what the terms would be.
"That's too much uncertainty for us.To just believe it will all be OK isn't a risk we're willing to accept.
"So, if there is a vote for independence on September 18, on September 19 we will start making arrangements to relocate within the EU, and that would most likely be to the Czech Republic."
Mr McFarlane said: "We wouldn't relocate to England because if Scotland was independent it would almost certainly have a Conservative government and that then triggers a referendum on EU membership."
He continued: "I wouldn't say it's going to destroy the company, the company would continue to trade because it would adapt.
"But I would rather keep the jobs in Scotland and we would probably lose about 25 to 30 jobs out of Scotland to the Czech Republic."
He also said the company had put plans to expand its warehouse at the Livingston site on hold till after the referendum.
"It wouldn't make sense to build a warehouse if we're going to move elsewhere," Mr McFarlane stated.
"So, we're having to sit on our hands until September 19. It's holding us up."
He spoke out on the issue as Scottish Labour finance spokesman Iain Gray visited the site.
Mr Gray said: "Endura is building a business on exports, on innovation, on cutting-edge design, and this whole debate is damaging its business."
He added: "A lot of the debate about what companies and businesses might do following a Yes vote in September has tended to focus on large companies.
"But most businesses in Scotland are small to medium enterprises, and they account for over half of private-sector employment."
Mr Gray said that many other small businesses also had concerns about the impact of independence and said: "This could potentially have a very significant impact on the economy across Scotland."
A Scottish Government spokesman said: "An independent Scotland will continue in European Union membership, and the only threat to that status - and Scottish businesses' access to a single market of more than half a billion people - is Westminster's proposed in-out referendum on EU membership, which threatens to take Scotland out of Europe against our wishes.
"The purpose of independence is to ensure Scotland's immense economic strengths and huge resources help build a fairer and more prosperous society, encouraging business growth and ensuring firms such as Endura thrive."
David Cairns, executive chairman of Prismtech and member of Business for Scotland, said: "Mr McFarlane is right to be concerned about remaining in the EU and the only way to guarantee that is independence.
"Both David Cameron and Ed Miliband have been talking about the circumstances that would lead them to hold a referendum on leaving the EU.
"The uncertainty of having both a government and an opposition swithering and dithering over such an important policy is damaging for business.
"My companies trade across the world and across the EU on a regular basis and I know how important it is to stay in Europe.
"Scotland will be an independent member of the EU on independence day in 2016 and the UK looks to be heading for the exit door shortly after that.
"The only way to guarantee smooth trading with the EU in 2017 is independence.
"As Professor David Bell of Stirling University noted recently, Scots have a higher disposable income than most citizens of the Scandinavian countries and the Republic of Ireland, and of large chunks of the UK.
"Scotland is a good place to do business and it will be a better place to do business after independence."