Firstly, and most importantly, non-disclosure of material facts can have tragic consequences that follow a person for a long time. This community recommends always disclosing all material facts. The important thing for this question is deciding whether or not a railway penalty fare is material.
From reading this gov.uk guidance on "Good character requirement" for Naturalisation as a British citizen, Sections 2 and 3 are about "Criminal convictions".
3.2 Fixed Penalty Notices, Penalty Charge Notices & Penalty Notices for Disorder
Fixed Penalty Notices, Penalty Charge Notices and Penalty Notices for Disorder are imposed by the Police or other authorised enforcement officers for traffic rule violations, environmental and civil violations.
Railway employees are not listed as among those who are allowed to issue Fixed Penalty Notices.
Penalty Charge Notices are only issued for parking offences.
The only Penalty Notices for Disorder (see section 7 of this Ministry of Justice document on them) which are related to railways are for trespassing on the railway or throwing stones at trains. Getting on a train without a ticket is not trespassing on railway. Trespassing on a railway is walking along the tracks.
The crux here is therefore whether a railway penalty fare is a criminal conviction.
- Fare evasion is contrary to the Regulation of Railways Act 1889 (2.1)
- Penalty fares are legally regulated by section 130 of the Railways Act 1993, which in subsection (2)(l) states that the penalty fare is a civil debt.
- A "penalty fare" is therefore no different from your water utility charging you extra for their handling cost of you paying too late. Nothing happens legally unless you refuse to pay and eventually it gets taken to court to get an injunction on your income (and even then it'd be a civil, not criminal, case).
The conclusion is therefore that, having paid this penalty fare, there is no criminal conviction. It does not need to be declared on your visa application.
Seeing as you've identified your penalty fare as possibly being relevant for disclosure, then as far as I can see there would be no harm in declaring it. I believe including it is less risky than not including it, and should make you less worried about it.
Should it not be relevant, I expect it would be ignored by the decision maker. Should the decision maker decide it is relevant, then according to the gov.uk guidance linked above:
The decision maker will not consider these unless the person has:
a. failed to pay and there were criminal proceedings as a result; or
b. received numerous fixed penalty notices which would suggest a pattern of behaviour that calls into question their character.
Your penalty fare therefore should not affect your chances of getting a visa.
This answer draws on contributions from many in comments. Credit to Janus Bahs Jacquet, Tor-Einar Jarnbjo, jwenting and Gayot Fow
NB The document this answer is based on is probably not applicable to visa applications, although it is from the UK Visa and Immigration pages. This answer was previously deleted once this was realised, but the answer was reinstated by the community. Immigration Rules Section V3.4 and V3.5 is probably more appropriate, and this only mentions criminal convictions, never mentioning any sort of Penalty Notice.