Basel
2012–13 season
Swiss Super League club Basel had been monitoring Salah for some time, and after the Port Said Stadium disaster the club organised a friendly match with the Egypt U-23 team. This match took place on 16 March in the Stadion Rankhof, in Basel, and despite Salah only playing during the second half, he scored twice. The game ended in a 4–3 win for the Egypt U-23 team. Basel subsequently invited Salah to remain in the city for a week's training. On 10 April 2012, it was announced that Salah had signed for Basel on a four year contract starting from 15 June 2012.
Salah scored on his unofficial debut on 23 June 2012 against Steaua Bucureşti during a friendly match, a 4–2 defeat. He made his official Basel debut in a UEFA Champions League preliminary stage match against the Norwegian club Molde on 8 August, coming on as a substitute in the 74th minute. He made his league debut on 12 August against Thun, playing the full match. He scored his first league goal a week later, the second goal in the 2–0 home win against Lausanne. Salah scored his first Europa League goal in the quarter-finals on 11 April 2013, as Basel advanced to the semi-finals by beating Tottenham Hotspur 4–1 on penalties after a 4–4 aggregate draw. In the semi-final on 2 May, Salah scored against Chelsea at Stamford Bridge, although they were beaten 2–5 on aggregate. Despite late disappointment in Europe, Basel comfortably won the Swiss Super League season 2012–13 Championship title and finished runners-up in the Swiss Cup.

2013–14 season
Salah scored on the first appearance in 2013–14, against Aarau on 13 July 2013.
He scored his first Champions League goal a month later against Macabi Tel Aviv FC on 6 August 2013 in the third qualifying round. Before the first leg on 30 July, 2013, Salah did not take part in the UEFA-mandated pre-match handshakes with Macabi players, instead changing his boots on the opposite end of the pitch. Basel called the incident a "coincidence" and denied it was intended as a snub. Salah had been pressured by public opinion in Egypt to avoid shaking hands with players from the Israeli club. On the return leg in Tel Aviv, he took part in the handshake line, but offered fist bumps rather than an open hand to Maccabi players.
He scored twice against the Bulgarian league champions PFC Ludogorets Razgrad on 21 August 2013 in the play-off round. On 18 September 2013, Salah scored the equalizer against Chelsea in the 2–1 away win during the group stage, During the return tie on 26 November at the St. Jakob-Park, Salah scored the winning goal as Basel beat Chelsea for the second time with a 1–0 home win.

Chelsea
On 23 January 2014 Chelsea announced that a deal had been agreed with Basel to bring Salah to London for a fee reported to be £11 million, with the player scheduled to undergo a medical and agree to personal terms. On 26 January 2014 Chelsea announced the signing of Salah, making him the first Egyptian to sign for the club.