Deutsche Bank said the scale of the impact would depend on what monetary option Scotland ends up with, with a continuing currency union seen as "the least negative" option.
All major UK parties have ruled out sharing the pound with an independent Scotland, despite the Scottish Government's insistence that it would be in the best interests of both nations.
Unilateral use of the pound or a separate currency is the most likely option if a sterling-zone is denied, while the euro is "one of the least attractive options" and a "distant possibility", Deutsche Bank said in a research paper on Scottish independence.
While Scottish independence would be "bad for sterling" the currency may benefit from "a capital flight to the continuing UK", with Scottish firms relocating south of the border and propping up the pound.
Deutsche Bank said: "Whatever decisions might be made in the aftermath of a vote in favour of independence, with the rest of the UK being Scotland's most important trading partner, it will be important that any negotiations leave Scotland in a financially viable position.
"When it comes to the impact on the financial markets, we suspect that the period of uncertainty during the negotiation phase that a Yes vote would generate would be negative for both gilts and sterling."
It added: "Political uncertainty during the negotiation period is likely to be negative for the currency, with the scale of this depending on what monetary policy option Scotland eventually plumps for.
"A sterling currency union may prove the least negative, as it leaves the size of the economy covered by sterling the same and a formal agreement could help reduce the political risk premium.
"Sterlingisation could potentially be worse for the currency given the presumably greater chance of Scotland eventually ditching sterling in favour of a new Scottish currency.
"Euro membership for Scotland would reduce the size of sterling's coverage which in turn may be more negative for sterling, while a new currency could potentially be worst of all for sterling as in addition to reduced coverage, trade becomes more costly than the cases of retaining sterling/shifting to the euro, and the sterling area current account deficit would be higher thanks to the loss of oil exports.
"While it seems likely that an independent Scotland would be bad for sterling, particularly in the near-term as political negotiations take place, an offsetting positive impact might be in the form of capital flight to the continuing UK.
"The risk of capital flight following independence (or even following a Yes vote) may make a formal currency union difficult to sustain, just as was the case with the Czech/Slovak monetary union in the early 1990s which lasted just six weeks before breaking down.
"The failure of Scotland to assume its fair share of the national debt along with the risk of a depreciation in a new Scottish currency could also trigger capital flight by worried savers ahead of any decisions being made."
Scottish independence is also likely to herald constitutional changes at Westminster, and potentially another general election immediately after Scottish independence day, Deutsche Bank said.