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I have completed a Ph.D. in India, which is my native country, and am applying for post doc positions in the UK. However, due to strict visa rules, I am not sure if my application would be shortlisted. In these types of situations, my CV and application file have already been approved by the PI.

However, do universities generally sponsor non-EU candidates like me or is it the responsibility of the PI to make the proper arrangements? How can I ensure that my job is not denied due to non-academic reasons like visa issues?

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tl;dr: Read the job description.

Details: The job you're applying to is advertised publicly, and as a part of a job description it is normally explicitly stated whether or not the particular University is willing to sponsor the visa application for the non-EU candidates. If unsure, ask the contact person or/and their HR department.

If the university invites only those having a right to work in the UK to apply, there is nothing you can do about it — find another position to apply.

If the university is willing to sponsor the work visa for a candidate, there is nothing you (and your PI) need to worry about — the process will be handled by their HR department. Just make sure you meet Tier2 visa requirements.

Note that there are certain conditions for the University to apply for a Tier2 visa. Normally, the position should be advertised for at least 1 month. Also, the University should be a Tier2 sponsor (check the list).

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I just want to ask to Dmitry's answer:

  • Beside Tier 2, Tier 5 is also an option for post doc (actually most post docs I know are in Tier 5). Compare to Tier 2, Tier 5 is much easier and faster to get, and it will cost the university less (if any). Moreover, only a limited number of Tier 2 visas will be issued per year. However, if you intend to apply for permernant residency, then the time in Tier 5 will not be counted, you need to stay 5 years under Tier 2.
  • Most university will not require you to have a working visa (Tier 1, 2, 5) to do a post-doc. Even if you already have one, you still apply to a new visa when changing the sponsor.
  • To know if the university will sponsor the visa, reading the job description is not enough. You need to ask the PI. My own experience: I once applied to a post doc which stated clearly in job description that applicants have to show proof of work permit in the UK on the interview day. I didn't have one, because I'm a Tier 4 student. But it turned out it was not necessary, and many applicants did interview via skype from their home country.
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I believe that if the PI accepted your application, he/she knows they can accept international applicants. You should just make sure this is the case by emailing the PI directly about this.

Once you get the offer, it is still not certain that you get the visa. The UKVI (UK visa and immigration) authority and the university giving you the so-called COS (certificate of sponsorship, which is a requirement to get the UK visa (Tier-2)) are two totally independent entities. This means that the UK university cannot guarantee you'll get the visa.

For most cases you should get the visa, however because of many factors, most prominently inefficiency and mistakes made by UKVI, your visa might get delayed.

It is also quite rare that the university will pay you for issuing the visa as far as I know.

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