A Beretta 92FS is used by a CIA agent in their London safehouse in the series premiere "Leland Bray" (S1E01). Kyrgis police use them as their sidearm with Tom and Matias using them in "Kevin Jensen". An armed man confronts Tom with the 92FS in "Hostages".
CZ 75 SP-01 PHANTOM
What appears to be a CZ 75 SP-01 PHANTOM is used by a FSB agent named Cynthia Stegner (Kelli Barrett) in "Independence, U.S.A." (S1E03).
Glock 17s are used by Tom Keen, aka Christopher Hargrave (Ryan Eggold), and Nez Rowan (Tawny Cypress) as their sidearms. Black site officers use them with Andre Zidane (Afrim Gjonbalaj) taking one as his sidearm. Susan "Scottie" Hargrave (Famke Janssen) uses it in "Whitehall". Some of the HA assaulters use them in "Whitehall: Conclusion" when the building gets raided.
Glock 19
The Glock 19 is used by Matias Solomon (Edi Gathegi) as his main sidearm before he changes it to a SW1911SC. Nez uses one with a suppressor as her alternate sidearm, first seen in "Operation Davenport" with Jeremy Wallace (Ryan Woodle) using one with no suppressor. Ex-Army Ranger soldier Aldon Braddock (Jim Parrack) uses it before Jennifer Lin (Emily Chang) takes it in "Borealis 301". Tom uses it in "Whitehall" while on the run.
Kahr K9
A Kahr K9 with a suppressor is used by Tom in "Operation Davenport".
SIG-Sauer P226R
A SIG-Sauer P226R is used by an armed man in "Hostages". A HA tac team operator guarding the entrance to a black site in "Whitehall". It's also used by some HA assaulters with Tom using it in "Whitehall: Conclusion".
SIG-Sauer P250
A SIG-Sauer P250 is used by a CIA agent in London in "Leland Bray".
Smith & Wesson SW1911SC
A Smith & Wesson SW1911SC is used by Solomon while masquerading as a flight attendant before ex-Navy SEAL commando Frank Slater (Nick Basta) uses it in "Borealis 301", as main sidearm.
3D Pistol
3D pistols are used by hijackers in "Borealis 301", but are not fired.
Unknown
Assault Rifles
AK-47
The AK-47 is seen with Kyrkis police as their main assault rifle with Tom and Matias using them in "Kevin Jensen". Russian soldiers and OMON officers use them in "Independence, U.S.A.".
AKS-47
AKS-47 assault rifles are used by Kyrkis police officers in "Kevin Jensen". Some Russian troops use them in "Independence, U.S.A.".
BCM CQB-11
The BCM CQB-11 is seen with most of Rocha's men throughout "Hostages" (S1E06).
Colt Model 933
What appears to be a Colt Model 933 is used by a NYPD ESU operator in "Operation Davenport".
Enfield L85A1
An Enfield L85A1 is seen with a Halcyon Aegis mercenary in "Leland Bray" (S1E01).
Heckler & Koch HK416
The Heckler & Koch HK416 is used by a CIA agent in "Leland Bray". US Marines stationed at the Kyrkis embassy use them in "Kevin Jensen".
IMI Galil MAR
IMI Galil MARs with Meprolight scopes and suppressors are used by hired mercenaries sent to assassinate Brian Mayhew near the end of "Operation Davenport" with Nez and Tom using them from mercenaries they disarm.
Norinco Type 56
Norinco Type 56s are used by Tom and Matias in "Keven Jensen" while they try to escape from Kyrkis police.
SIG P556 SWAT/SG 550 Hybrid
A hybrid of a SIG P556 SWAT on a SIG SG 550 series lower receiver is used by a Marine in "Kevin Jensen", which is an odd weapon considering that most of them use HK416s. A few of these rifles fitted with ACOGs and suppressors are used by hired mercenaries sent to assassinate Brian Mayhew at the end of "Operation Davenport".
PTR 32P PDW R
PTR 32P PDW Rs are used by HA tac teams when they breach a victim's residence in "Independence, U.S.A.".
Shotguns
Mossberg 590
A couple of Mossberg 590s were used by Tom in "Borealis 390" after the flight was hijacked.
Grenade Launchers
ICS-190 AGL
An ICS-190 AGL is used by Solomon to fire smoke and Tympanic Bursting Device 40mm grenades in "Hostages" during a hostage rescue op.
Mk 19 Grenade Launcher
The Mk 19 Grenade Launcher is seen mounted on a US Marine Humvee in the American embassy in Kyrkistan in "Kevin Jensen".
Sniper Rifles
Savage Arms 10 BA
A couple of Savage Arms 10 BAs are used by Nez and Solomon in "Hostages".
A Palmer Cap-Chur Short Range Projector is used by one of Diego Rocha's men in "Hostages" (S1E06) prior to transporting Tom to him. Tom and Nez use them when the former leads a raid on the HA building at the end of "Whitehall: Conclusion".