From İzmir: Take the TCDD train from İzmir Basmane or İzmir Alsancak station to Selçuk — the journey takes about 1.5 hours and trains run several times daily. From Selçuk, the ruins are about 3 km away; taxis are available, or it is a manageable walk in the morning. This is the cheapest and most scenic approach.
From Kuşadası: Dolmuş minibuses run regularly between Kuşadası and Selçuk (about 30 minutes), and from there taxis serve the site. Many visitors coming from the coast arrive this way. Kuşadası is the cruise ship port, so expect company.
From İzmir by car or bus: The D550 road south from İzmir reaches Selçuk in about 1.5 hours. Direct buses from İzmir's main otogar to Selçuk run frequently. Note that the main Ephesus site has two entrances — upper (south) and lower (north) — and it is worth entering at one and exiting at the other if you have transport flexibility. Most visitors enter at the lower gate and walk uphill toward the Library.
On site: The main archaeological site, the Ephesus Museum in Selçuk, the Basilica of Saint John, the İsa Bey Mosque, the Temple of Artemis column, and the House of the Virgin Mary are all within a 10 km radius but not walkable between them. Taxis are the simplest way to cover all sites in a day; negotiating a set rate for a circuit works well.