Samuel Armstrong, 23, of Copt Hill, Danbury, Essex, is charged with two counts of rape and one of sexual assault.
He has been suspended from his position as chief of staff to South Thanet's Tory MP Craig Mackinlay.
The charge follows an alleged incident at Parliament in October.
Mr Armstrong was bailed to appear before Southwark Crown Court on 28 April.
He was ordered not to enter the Palace of Westminster and not to contact the alleged victim.

The county council plans to prohibit buses, taxis and private hire vehicles from using Queen Street.
Oxford Bus Company said the authority needed to consider the "additional pressure" on surrounding streets.
The council said it was "vital" for more pedestrians and cyclists to use the route.
Oxford bus Company said: "We can't have a situation where Queen Street is pedestrianised but the additional pressure put on surrounding streets means that waiting conditions for bus passengers become unbearable, or walks between stops become unacceptably long - or our customers can't get taken to where they want to go.
"A credible, agreed plan therefore needs to be identified between all parties before Queen Street can be closed and dialogue is ongoing to achieve this."
Oxfordshire County Council said the street was one of the main routes across the city centre and added pedestrian and cycle numbers were expected to increase "significantly" in the future due to development across the city.
"It is vital that strong pedestrian and cycle links are maintained and encouraged, and improvements to the pedestrian experience are made, to ensure a well-connected and joined up city centre that will continue to thrive," it added.
A consultation on the proposals runs until 6 June.

An administration oversight allowed US student Sanmay Ved to buy the right to control the domain on 29 September.
The oversight left him in charge of Google.com for about a minute until Google caught on and cancelled the transaction.
Now Mr Ved has been given a cash reward for spotting the error, which he has decided to donate to charity.
Google declined to comment on the story.
Mr Ved detailed his experience in a post on the LinkedIn site saying that he had been keeping an eye on Google-related web domains for some time because he used to work at the search giant. Mr Ved is currently an MBA student at a US college.
In the early hours of 29 September he noticed a for sale sign next to the Google.com name while browsing sites on Google's own website-buying service.
He used a credit card to pay the $12 (Â£8) fee to grab google.com and got emails confirming he was the owner. Almost immediately he started getting messages intended for Google's own web administration team.
This was followed by a cancellation message sent by the website buying service which said he could not take over Google.com because someone else had already registered it and his $12 payment was refunded.
Now it has emerged that Mr Ved has been given a "bug bounty" by Google's security team for revealing the weakness in the domain buying system. The internal emails Mr Ved received while in charge of google.com have been passed to this team.
Mr Ved decided to give the cash to an Indian educational foundation and in response, Google doubled the reward.

It says Berlin should consider raising the retirement age to that level by 2060, from around 65 at the moment.
The central bank says that otherwise the country may struggle to honour its pension commitments.
It points out that the state pension system is in good financial health at present, but will come under pressure in coming decades.
The Bundesbank says that as baby-boomers - those born in the post-World War Two period - retire, there will be fewer younger workers to replace them.
The retirement age for Germans is set to rise gradually to 67 by 2030.
However, the bank believes that from 2050 this increase will not be enough for the German government to keep state pensions at their target level of at least 43% of the average income.
It is therefore proposing pushing the retirement age up to 69.
"Further changes are unavoidable to secure the financial sustainability (of the state pension system)," the Bundesbank said in its monthly report.
But German government spokesman Steffen Seibert said they stood by retirement at 67.
"Retirement at 67 is a sensible and necessary measure given the demographic development in Germany. That's why we will implement it as we agreed - step by step," he added.
An aide to a Kent Conservative MP has appeared before Westminster magistrates charged with rape following an alleged attack at the Houses of Parliament.
[NEXT_CONCEPT]
A "credible plan" needs to be agreed before any move to ban buses and taxis from a street in Oxford is made, a bus company has said.
[NEXT_CONCEPT]
A man who briefly bought and owned the Google.com web domain has been rewarded by the search giant.
[NEXT_CONCEPT]
Elderly Germans may have to keep working until the age of 69 if a Bundesbank proposal is adopted.